I guess my question is: It smells of what, exactly?
If it is a plastic or chemical smell, then it probably has to do with the material of the bottle itself either off-gassing or breaking down. That could be hazardous (v. unlikely) or maybe just unappetizing. If that is the case, then I'd look around for another brand of water bottle.
On the other hand if it has a foul organic odor - smelling like mildew or rotten eggs - that would indicate that fungi were starting to grow, or that sugars or material was beginning to rot. If that was the case, then you need to address the way the bottle is cleaned. A common household bleach solution will kill most anything, but simple hot water, detergent, and a decent brush will help. A white vinegar solution will also kill most bacteria, as well as dissolve any mineral deposits.
I take a water bottle or two with me on just about every workout, including my all-day bike rides. You are right to be concerned about the sanitation of your drinking water, but I'd advise against being overly sensitive. If you get thirsty enough, you won't really care if your waters smells - or tastes - a little "plasticky." But you don't want to be drinking so much as a drop of water contaminated with e-coli or other pathogens.