ptolisa - sounds like your group has made a conscious decision to operate under the district's control, but your posting has a few misstatements. I had to go look this stuff up myself; it gets very confusing, but there's lots of people who look here for advice so it should be as accurate as possible.
The fee to become a federally-registered tax-exempt entity is a ONE TIME fee, not an annual fee. It is $300 if your group's gross proceeds are less than $10,000, and $750 is you're over $10,000. Notice that's GROSS proceeds, not net. So if your PTO holds a fundraiser that takes in $13,000, you're over the $10,000 mark even though you only get to keep 50%.
The threshhold for whether or not you should even consider applying for 501c3 is $5,000, not $25,000 as you suggest. The IRS would like any group that normally takes in over $5,000 annually in GROSS receipts (again, we're not looking at net profit, but rather total money in) to register for 501c3.
An example. For the past few years, ABC PTO has taken in gross about $7,000 from various fundraisers, yearbook sales, and dues, even though they profit only about $4,000 each year. It's time to formalize as a 501c3. They will owe a one-time application fee of $300 to the IRS.
This overly simplistic approach ignores filing for state incorporation, but those fees are typically less than $100 per year.
A wise man told me that whoever owns the tax id number under which money is kept in a bank owns the money, regardless of how things are perceived. That would suggest the city or district actually has claim to the money kept in PTO accounts opened with their tax id number. Since all the other PTOs in town do the same thing, it's probably been done this way for a reason. Presumeably, the dsitrict or city is taking care of your tax reporting, for example. However, sometimes PTOs are under the impression that they can use the school district's tax id number with no risk or obligation. In our PTO's case, the original bank account was set up using the school's tax id number simply because the treasurer didn't know any different. Thankfully, it's become a lot easier to get info about this stuff (thanks, Tim!).
Even if it's not necessary for your PTO to formalize as a 501c3, you might want to consider getting your own tax id number. There's virtually no obligation but it gives your group legal ownership to your bank account. It's free, it's easy (go to Form SS-4 from
www.irs.gov).