I always take an empty bottle, and have found some ways to eliminate virtually all hassles (but even when I was hassled, I've never been denied):

1. Keep the bottle out of sight. Non-TSA queue-keepers like to make up rules. Plus, you increase the hassle-factor if more screeners other than the one manning the X-ray monitor see the bottle ("Ze're wata in that?").

2. Take off the cap.

3. Keep the bottle away from clothing in your bag. I've had a screener tell me this makes it harder to determine if there is liquid in the bottle.