I'd use polyflex.
it's as safe as everything else - which is to say that it's down to the individual to take reponsibility for drinking from a 3d printed cup.
But shouldn't taint the water as much as a tpu based material.

Actually there IS a safe flexible material that is not only anti-bacterial but also anti-viral.
No it's not certified - but it'll kill any microbes that come minto contact with it.

reprapper techs flexible pla with copper.
Copper kills any and all microbes that come into contact with it.
http://reprapper.en.made-in-china.co...-Filament.html

Not sure how it would effect the taste of any liquid - but it would be safe from a bug point of view.