I've found that most dogs really dislike being photographed (that is, if they know they're being photographed). I think it's probably that thing, that massive clunky thing you put up in front of your face that freaks them out. The flash and the lights don't help. But as much as your dogs love you, I'm afraid they probably don't love your camera.
There are a few ways around this. Sleeping dogs shots, of course :) but there's only so much you can do with those. Another trick is to mount the camera onto a tripod, or rest it on something solid, and use a remote (if you have one) one the dog is in frame, so that your face is recognizable and your dog can stay in his/her safe zone.
If you don't have a remote, you can still manage this by just framing the dog, then lift your face away from the camera so he/she can see you. Seeing your face, of course, is the best thing in the world to your dog.
Give it a shot. You may end up with fewer of those guilty, sort of "what did I do" faces and more dog smiles.
And we all know that dog smiles make the world go 'round.
