Nothing wrong with running a virus check on your phone.
But it is probably just a scam.
No real legit site will ever popup and tell you that you have virus's on your phone, and honestly, wouldn't care.
Its a fear tactic scam, don't be fooled into clicking or downloading anything.
I got a hilarious one the other day that said the battery of my "Generic Android Device" had been infected by a virus!
@mikekatip: That's a nice burn. A schoolyard insult for the smartphone generation. :p