As a germ-a-phobe and a person who stays in hotels for a living (I'm a flight attendant) you can be proactive, but you have to surrender to certain things. Germs are everywhere, even in the 5 star luxury resorts! Here is my routine:
1. I automatically check for bedbugs. (biggest tip: check the seams and piping of the mattress, if you see small black reddish spots that is excrement from a bedbug. EWWWW!!!! After freaking out, get a new room immediately!)
2. I peel back the comforter. You don't know the last time that thing was washed. (Google blacklight hotel comforter for more gruesome info.)
3. Inspect the sheets. Make sure they have been changed. I've found hairs, dirty band aids, and blood spots over the years. Pull them down, check out what your slipping into before it's too late. And don't forget the pillow cases. (Also, if they have a decorative pillow, that thing immediately gets tossed to the chair or couch. Not staying on my bed, no sir.)
4. Don't touch the floor with bare feet! I bring washable slippers. You have no idea what is lurking on that floor. (As previously mentioned, google blacklight hotel room for more info.)
5. I don't use the coffee maker if it has a carafe. I have no idea when that thing was cleaned. If they have the new kind in which your cup is the vessel (ie. Keurig) then I'll check to see if the machine is clean.
6. The remote. Oh the remote. That was found to be the most disgusting item in the room. Bring disenfecting wipes and clean it. Or, if you forget them, here is a handy tip. If you don't use the ice bucket, take the bag they give you for it and put it on like a mitten. Pick up the remote with that hand and turn the bag inside out and voila, your remote has a shield!
7. Toilet, I always give the seat a quick wipe down. Never hurts.
8. Tub. I check for strangers hairs and wash 'em away. I've been caught in the game of "follow that hair" while showering one to many times. It's not a fun game.
9. This is my paranoia but I never leave my toothbrush out. Don't know if it is urban legend about housekeeping using a guest toothbrush to clean the toilet

, but just the mere thought of it makes me shudder. I'll pack it away for safe keeping just to be sure.
I know, I said you have to let go of some control, but after doing this for 15 years this routine is done in 5 minutes flat. Am I missing things? Sure --light switches anyone??

But at some point you have to surrender. This is just enough to protect myself without going overboard.
Disney hotels usually been on the higher end of clean, but no hotel is spotless.