I always assumed it had something to do with regular car insurance rates dropping at age 25, as you're considered an "experienced driver" by then. Since the insurance is higher for an under 25 driver, the car rental company has to charge the under 25 person more. (off topic a bit, but IMHO, it should be more like after having your license for x number of years with no accidents. I got my license at 23, and got my insurance lowered at 25. I was grateful, but I didn't feel like an "experienced driver"!)
When we were in college, my friend would rent through rent-a-wreck because they were always cheap, even with being under 25, so that might be an option if you don't mind a clunker!