I would tell you, but you might invade my charming rural town.
Yup. Though I’d say that Zionsville is a better fit for the “charm” part, if not small town part (it’s a growing suburb, but the downtown is straight out of the Saturday Evening Post).
And if Google is to be believed, places like Greenfield, New Palestine (cute downtown, not so charming), Whitestown, Noblesville (mostly suburbia now), Whiteland, etc. are all within the 30 minutes. Though I’m searching at 10:45pm, not during rush hour.
Woodstock, IL, is a quaint town, predating the Civil War, with a charming old-school town square* and nearby farmland but also decent daily Metra service to downtown Chicago. Not quite a half-hour, but less than an hour by express train.
*Charming and old-school enough to play Punxsutawney in Groundhog Day. 
Sorry, actually a bit over an hour by express, but you can sleep, read, etc. instead of being hunched over a steering wheel.
San Juan Batista is only “charming” for very small values of appeal. And Morgan Hill/San Martin is really just an exburb of San Jose at this point. However, Half Moon Bay is just over Santa Cruz Mountains from San Mateo, so if you consider the entire peninsula to be “San Francisco” and fancy a speed run across Hwy 92 it theoretically meets the o.p.’s qualifications, though I defy anyone to make good time during peak traffic hours.
Stranger
Not quite rural and not quite 30 minutes. Boston. Carlisle MA is at the 35 minute mark and has quite a rural feel, farmland, no chain stores, barely any commercial property. Stow MA is 45 minutes, large undevolped areas of land, 3 golf courses, one strip mall. Step a little further out and the towns get pretty rural. At an hour out you’re in the middle of nowhere.
On a drive from Long Island to Buffalo, I realized that NY State is way more rural than I had been led to believe. Interestingly you don’t get the same impression in California or Florida.
I came here to mention Carlisle, too. It’s a bit further away than the requirement but it’s the friggin’ sticks. Population under 5,000 people. The minimum allowed lot size is 2 acres but 5-plus-acre properties are common. The town is considered to be nearly completely “built out”, meaning that there are few suitable undeveloped lots available.
I’m from a charming village in Ohio, but it’s more than 30 minutes to Columbus.
I’d suggest Granville, Ohio.
St.Paul/Minneapoli
According to the population signs, Minneapolis is only 300,000 people, but, im positive its well above that.
Drive 30 minutes in either direction of Minneapolis and there are tons of nice towns with populations between 1,000 and 10,000
Oh, grasshopper…
I once arrived in Cleveland at the beginning of spring and wondered why the people were so nuts. I mean, they were running out and drowning in Lake Erie, and other lesser lakes, like lemmings. Then I endured a Cleveland winter and I understood.
Upstate New York is largely rural outside of Buffalo and Rochester. A lot of the early industrial cities like Schenectady have declined precipitously compared to national population growth, and nearly twenty percent of the land is state parks or preserves even though New York doesn’t have any major National Parks or Forests.
There are plenty of areas of California that are decidedly rural, particularly in the north and east, although you may not get that impression if all you’ve seen is is the sprawls of San Francisco, San Diego, and Los Angeles. However, those areas are several hours outside of the major urban cities because of how much suburbia there is. The Kings Range/Life st Coast are can feel as remote as anywhere in Wyoming once you get away from the highways.
Stranger
I’m not hung up on Lancaster specifically. In all reality, its the small towns immediately surrounding Lancaster I’m really talking about. Lancaster’s too small to qualify as the “big city” and really a little too big to qualify as the “small town” (though as I said I’d happily live there if it was closer to Philly - it is really close to farmland and proper small towns).
Front end web development. I know all the big players in Wilmington and haven’t been able to get my foot in the door.
I drive up 202 to Collegeville for my work 2 days a week. I haven’t seen anything on the way that really fits the bill, and it’s still too far from Philly. I’ve considered moving to Westchester. It would make my current job easier, but again, too far from Center City if I had to work there. I am currently a consultant and am at a different place every few years.
I don’t know if it meets the OP’s criteria, but Mount Dora’s Wikipedia page actually mentions its reputation for “small town charm” and it is within 30 minutes of parts of Orlando (metro population 2,387,138).
Kinda.
Chappell Hill is about 45 minutes NW of Houston. Primo bluebonnet viewing area and lots of small antique shops.
Any more opinions on what counts as “charming” within reasonable commute of RTP? I just got a job there, after moving to Chapel Hill for my wife’s job. We definitely like it here, but housing is relatively expensive and the rush hour drive to RTP is just barely tolerable. However, most of the areas closer to RTP that I’ve explored (SE Durham, Cary, Morrisville, etc.) seem to have few virtues other than proximity and price.
I think the key to working in Center City Philly while living in a more rural area is access to SEPTA Regional Rail. Lots of more rural areas in the Lansdale area (Hatfield?) and the train runs to Lansdale. Unfortunately, when SEPTA took over the old Reading Railroad as part of their Regional Rail system, they terminated the Reading line in Norristown instead of farther out - otherwise Collegeville would be on the line. Other than distance to Center City Collegeville would meet your criteria.
ETA: Now that PennDOT is finally close to finishing the 422 improvements over the Schuykill, King of Prussia/Malvern are going to be a more comfortable commute from the Collegeville/Royersford/Trappe area.
If your looking for a place like you see in movies probably not.
I consider parts of Ellicott City MD charming.
I lived in Morgan Hill for several years. The area is definitely still rural. You’ve got people riding horses down the main street and central town area is surrounded by farm land. It’s growing, and it’s not a small town, but you’ll feel relatively isolated if you live there.
Google maps is high. You’re not getting to Woodside from San Jose in 30 minutes unless everyone else gets off the road and you’re driving a fast car like you mean it.
I lived in the Santa Cruz Mountains for several years and worked in Cupertino. You could almost get to Cupertino in 30 minutes from a very rural area (pop 7500), driving a fast car, like you mean it. 
Eugene, OR would fit easily. Heck, drive 15 minutes and you’ve reached some tiny little agricultural something. The city just ends.
Portland, OR also fits, although the traffic has gotten so bad that 30 minutes is pushing it these days. Once you’re out of the city, you will quickly hit rural in any direction.