no they do not you have to take you antena off before you put the cover on

 

Mine came with a plastic grommet in case you want to make a hole in the cover for the antenna. But I wouldn't want to do that. It would probably allow some water in. Plus, it'd be a hassle when you put the cover on.

 

I took my antenna off to put my cover on and havent put it back on since. For some reason once i took it off putting it back on just made it look out of place.

 

^ Same here. But I have a billet shortie antenna and very rarely, I put it on if I'm going to a cruise night or something...