Agree partially, disagree partially.
The actual filing with the FCC indeed has no fee attached.
Creating a filing that has a fighting chance of resulting in a grantable construction permit isn't usually something that can be done without professional assistance, though. There are engineering filings that have to be made, and lots of details that can and will catch an applicant if he or she is going into the process as a novice. $2500 does seem steep to me (it's more than I charge my clients, for sure), but there is considerable skill and specialized knowledge that goes into preparing a grantable application, and that's worth something. (What's more, an applicant that can't come up with a very low four-figure sum to get its application right probably doesn't have the resources to build and then operate a station in the long run.)
I agree strongly with other posters here who've warned about the potential dangers of raising money for an as-yet-nonexistent nonprofit. I'd really, really want to be getting some advice from a lawyer who's skilled in these matters before I solicit or accept as much as a dime toward a project like this. At a bare minimum, I'd be talking to my state's division of charities or secretary of state's office to get some guidance on the rules. The consequences of violating some of those rules can be very serious.