I stand corrected....yes AU does do flight training, and I never knew that. However, I'm not 100% sure what's up with how they use it towards a degree. I would say to call the Aviation or Aerospace Dept and ask.
Cost depends on each semester--some may cost more, some cost less. However, you can look to spend about $4k to $6k, depending on fuel costs, which means you could pay anywhere from $100 to $160 an hour for single engine planes, maybe double that for mutli-engine planes. I know it sounds like a lot, but there is really no way of getting out of it anywhere you go. BUT, there is hope with federal student loans. That way you can pay it back after graduation when you may have a job.
Both schools are great schools and have great programs! My recommendation is that you go to MTSU because they have brand new, better aircraft--DiamondStar20's and 40's (with Garmin G1000 glass cockpits, which is important to get experience in for maybe later professional flying), Piper Archers, and Piper Seminoles. However, AU does have a good football program......
I hope this helps! Good luck!