Bottle contamination is a valid concern in some areas. Much of the MUP in my area runs alongside the Trinity "River," which is mostly just a tarted up flood control drainage ditch. It's often contaminated with e coli, salmonella and other cooties, forcing the suspension of some warm weather tubing festivities, such as the joy of floating in everyone else's urine while watching concerts at the amphitheater.
Then there are the horses. Kids and toasted frat boys and girls from the nearby college barfing along the trails. Cyclists and runners spitting and blowing snot rockets.
So I'm wary of every puddle along the MUP.
Hydration backpacks may be a bit safer, since the drinking end is above most of the contamination zone, and most hydration tubes have caps. But I use mine mostly for longer walks and jogging, seldom for bike rides.