The aliens hate our freedom.
Wait a minute.
You’re telling me that these aliens have discovered space travel, created massively powerful weapons of destruction, and yet would not be able to figure out where to attack?
Those are some mighty ADD aliens, if ya ask me.
a. The aliens in Independence Day had been snooping around for a while. Remember, they had lost the Roswell saucer during one of their scouting missions. Plenty of time to locate the tourist traps.
b. Anal probes. “Hey, what are you alien freaks sticking up there? The Washington Monument???”
The physical destruction of everything is pretty crude. A more subtle, yet effective, approach would be to pinpoint a biological weak link, as in this classic James Tiptree, Jr. (A.K.A. Raccoona Sheldon) short story.
They identify critical points to attack the same way Rowlf found the rest of the gang in The Muppet Movie:
(paraphrase from memory)
“I checked the script. Exterior. Desert. Night.”
I’m mostly thinking of metals. If you are after metals, cities would be the place for it.
Mars Needs…Bethlehem Steel?
John Travolta needed Gold. Maybe Phil the Martian needs some Bethlehem Steel.
[nitpick]Dr. Teeth and the Electric Mayhem. Rowlf was already with Kermit, et. al.[/nitpick]
They don’t look like Presbyterians to me.
And if someone somehow poisions the Central Valley… Bye Bye Veggies!
If those aliens were so damn smart, they would have taken out the airbases first. There would be plenty of time to level the cities after the defenses had been taken care of.
yeah, but why does it matter since every attack will result in 90%(at least) losses for Earth and the ship won’t be harmed anyway?
How were the aliens supposed to know that they had found the one planet in the entire universe that, by sheer conincidence, uses the exact same OS’s on their computers as they do,
Crap. That should be an “?” at the end.
Besides, the ID4 aliens could easily beat the crap out of the Signs Aliens, who were apparently as dumb as a poverbial post. Either that or the entire thing was a method of killing off their surplus population by dumping them on Earth.
You’ve gotta love the fact that an Apple laptop, which isn’t compatible with most Earth computers, can interface flawlessly with a totally alien spacecraft 
Maybe Steve Jobs is in fact an alien who crashed landed on earth, say…in 1947? He built the Mac to give the earth a fighting chance in the war.
That or perhaps Macintosh has been breaking tech export laws by selling Macs to creatures from other star systems?