There is a guy at my work who watches videos with the sound on in the stalls. It's very annoying. He also talks on speakerphone while on the throne.
As long as you aren't that guy, and you wash your hands and clean you phone regularly, you should be fine. My bigges fear would be dropping my electronics in the crapper. I've almost done this with my mp3 player.
I completely silence it when I'm in the crapper. I don't even really clean it. I'm not ******** on my hand and then using my phone. It refinds my pocket when wipe time rolls around.