Agree with Scott.

The camera goes over the shoulder with a strap designed for that purpose. The Upstrap works well. If you are using a long lens, place the camera "backward" on your shoulder, this will let the lens hang down against your body instead of sticking out and banging into things.

If you absolutely have to keep it in a case, take a look at the SLR cases from Think Tank Photo. They hold a D-SLR with an attached lens, ready to shoot, attached to your belt or your shoulder harness. The bags come with a waterproof cover.

Carrying your SLR in your backpack means you won't take many photos.

Finally, bring a small tripod, even if it's just a Gorillapod SLR model. You'll be happy you did.