Next May 08 we have an early flight out of Munich airport at 6:55 AM and the rental car return does not open until 6:00 AM which means we should probably return the car the night before. The problem is that most of the available hotels I have checked either do not have shuttles or have shuttles that start at 6:00 AM. I know there are options if I want to spend $400 a night but I am aiming for less - anyone who has been there recently have any ideas or suggestions?

I would try a Priceline bid for the Munich Airport. The Marriott (Priceline 4*) is, I believe, the only hotel with that rating in that zone on Priceline. Priceline bidders "win" that hotel quite frequently with bids ranging from $65 to $125. You've got time to make arrangements, and I think that's your best bet.