Most gas operated semi auto rifles don't use subsonic ammo because there's not enough gas with a suppressor installed to even cycle the bolt. Maybe with a badly designed suppressor, you would get gas fluctuation and reduced velocity in regard to supersonic ammo and reduced velocity. Generally though, suppressor's are made to work with both supersonic and subsonic ammo.
http://www.youtube.com/watch?v=PEoh-MmpJNM for example.
In regards to the comment above me, how would a suppressor slow a bullet down? For example, even if a suppressor expanded and trapped all the gas from a shot, it would be as though the bullet had simply left the barrel and was then traveling with it's own momentum. The Suppressor doesn't grab on or create friction on the traveling bullet in any way, it only creates a chamber for the gasses to expand in at a controlled rate so they create less noise. So how would a suppressor slow the bullet down?