As a photojournalist, I'm obviously keen to photograph as much as possible during the actual wedding ceremony. Unfortunately I occasionally come across a venue/registrar/vicar/priest who puts restrictions on what I'm allowed to photograph - sometimes banning it altogether!
This is usually because they've had a bad experience with a photographer being disruptive by either getting in the way, or using flash, or just generally being a nuisance. I like to reassure people that I don't use flash during the ceremony and, just like the rest of the day, I try to be as low-key and unobtrusive as possible.
I always recommend that couples bring this subject up with their chosen venue as early as possible and make it clear that you want your photographer to capture the ceremony. The worst case scenario is when both you and I expect to be able to get photographs during the ceremony and then are told at the very last minute that its not going to be allowed.