Most of the places I’ve worked where they used Cisco, they expected applicants to have training, experience & certification on Cisco stuff. Anybody who expected to get trained on-the-job wouldn’t make it past the phone interview.
You have no idea how many completely and utterly different OSes for completely and utterly different hardware platforms have been called DOS, do you? 
Java has a life beyond Oracle. It had a life beyond Sun, too, back when Sun was the main force behind it. It can be used to teach (one form of) OO, it can be used to teach (most) algorithms, and it can be run on a huge variety of platforms. You can use Java without using anything made by Oracle. (You soon might have to, given Oracle’s history in this space.)
Compare Java to AutoLISP, the AutoCAD programming language. It has no implementations other than AutoCAD. It is intimately tied to one use-case; namely, “extend AutoCAD”. It’s probably just as full-featured, after a fashion, but I guarantee you that the tooling surrounding it is lacking compared to what Java has. And, of course, you can’t use it without paying one company and being locked into their products. While I have no specific reason to hate AutoTools, I’m also not being paid by them, so I have no reason to boost their software.
If your school teaches Java to the exclusion of the theory behind CS (discrete math, data structures, algorithms, project planning and team organization, OSes in theory and practice, networking etc.) that’s a problem if they’re charging full price. Java Schools are McSchools which prepare people for McJobs. That doesn’t say anything about Java, but, as I said, some languages are inherently more prone to this than others.
We always have to separate theory from practice. Cisco routers and so on are as good a way as any to teach theory, but they’re only one aspect of the practical world, and they’re gratuitously different from the other products. College tuition is expensive, and if you’re paying to become one company’s customer first and foremost, you’ve wasted a lot of money.
I’m going back to lurking. Its a much safer world 
To me, the commands that I’ve used in formatting the Cisco routers and switches have translated into the other systems I’ve used. /? will get you halfway to what you’re trying to do in the systems I’ve used. Admittedly, all the systems I’ve used have been post-2000 a.d., so my history on the other systems is woefully lacking. The systems I’ve worked on, mostly Cisco, Linksys, Dell, and others, have had languages that are (A) mostly similar, and (B) easily researched on google. When looking up things on an unfamiliar system, I"ve been able to type in “What is netsh command in Netgear” and had similar results.
I should have used more expressive language when talking about the commands. But, in my experience, when I learn a new command under one system that uses a dos-like text-base command interface, there will be a congruent command on most other systems. Once you know the word exists in one language, you can usually find the same word in another location. Right now, Cisco has the most words for things, so they are the one to refer to, and the best one to learn because other folks copy what they do. The language I learned in programming Cisco has been easily, in my opinion, usable on other things. Half the battle is knowing that the proper command exists - like writemem. Always find the writemem before you turn it off… :).
Re-engaging cloaking field in 5…4…3…
In my biology training, I learned the theory behind a wide range of lab techniques and strategies. When I went job hunting, employers only asked how much hands on experience I had with, say, Illumina next-gen sequencing.
I have a lot of friends who majored in engineering fields at various schools. When I told them that my courses focused on Cisco they were shocked. Construction management classes aren’t “The World According To Cianbro”. A Mechanical engineering major isn’t “General Dynamics or GTFO”. What makes networking so special that it’s worthwhile to focus on one company?
Back in the day when IBM was the king of the hill in the computing world, they made it a practice to provide their mainframe systems at incredible discounts to many universities, if not practically free, depending on their strategic position in the academic hierarchy. That was back when they also encouraged using “IBM” as an adjective for “computer”, as in, “IBM machine” or “IBM cards”. Like, is there anything else?
When students graduating from these schools and going on to become executives in IT or general business were involved in computer acquisition decisions, guess what was the first company they thought of – and very often, the only company they thought of? Because, in fact, it was the only computer company they’d ever known or had any experience with.
Cisco could be playing the same game.
If you needed to create a course on how to use a desktop/laptop computer for people who had never touched one, but planned on a career in an office where they were expected to use a computer, check work emails, read documents and spreadsheets, how much time would you spend on Microsoft, and how much time would you spend teaching Linux and Mac? Your typical office drones are going to be using MS products so overwhelmingly that it just doesn’t make a lot of sense to spend much time teaching much else.
In networking, if you go into the field, you will almost certainly be using Cisco products. Some places may have a mix, but at larger companies the alternates are often “leverage” boxes–“See, Cisco, we already have some Juniper boxes so if you don’t give us a bigger discount on our next generation replacements, we may choose to go with them instead!”
Places that are completely Cisco-free will almost certainly be used to “retraining” Cisco people into all of the right syntax.
Probably none (wrt Cisco stock for your professor). Here’s the thing…Cisco, as has been pointed out to you, dominates the market. It’s got the broadest base, and basically if you learn Cisco stuff you can do most everything else. Teaching you on that equipment means preparing you for the broadest possible job set, since if get a job in IT you will almost certainly touch some Cisco equipment at some time. In addition, a lot of companies (such as HP for example) have essentially ripped off Cisco’s CLI. With a few weird exceptions, if you know Cisco IOS CLI you know Procurve CLI.
As for VoIP phones, again, CISCO is the leader in that tech and basically drives the industry. You could look at Mitel or Shoretel…but VoIP is VoIP, and what you SHOULD be learning is the theories behind how it works. The specific vendor is (or should be) pretty much irrelevant if you learn the fundamentals.
Basically, your teachers are teaching you on the hardware and software that’s the most used, but they are (or, again should be) teaching you the fundamentals on that equipment…and those work for any vendor. You just have to learn a vendors specific quirks for how they do X…and learning how Cisco does it will give you a basic understanding of how they all do it, in the end.
Because a network engineer isn’t really an engineer - by engineering standards. They are a technician - at least when it comes to configuring the technology. They may engineer solutions for IP telephony or routing or addressing schemes - but very little of that design work is vendor based - and the differences are picked up quickly.
Schools don’t have unlimited budgets for equipment and they don’t have unlimited time to teach coursework. Cisco is VERY generous in giving non profit educational institutions discounted equipment and they are the most common equipment in the marketplace - it makes sense to put your limited resources there.
Ask your friends how often they have to give a CAT backhoe operator specific instruction on how to dig a trench 20 feet wide and 100 feet long - up to and including which levers to pull when. Or how often they specify in the prints that all handtools will be Makita to ensure interoperability. Different disciplines, different needs. As someone who has hired router jocks and such many, many times - Cisco is king and all others are pretenders to the throne. Get your Cisco certs and you’ll get a job.