Everybody uses glass for water even if it does not kill bacteria. Shouldn't be the main factor to choose one over other. People must filter their drinking water and remove the pathogens before filling their drinking bottle in any case.

If this is not possible, take in mind that your immune system can take care about bacteria. In 99% of the cases after a learning period, local bacteria will stop being a problem. Unless your live in areas with very unsafe water sources or particularly dangerous organisms this shouldn't be a main factor in the choice.