I live in NYC and never leave my bike in my van while I'm here.

But travelling... I took my road bike and my mountain bike on a 3 week trip last year, including a week on Bike Tour Colorado with the MTB left in the back of the van.

In crappy neighborhoods, I make sure it's covered or not apparent in the car. If they don't see something to steal, the odds of a breakin are greatly reduced.

Finally, get a bike cover / bag. I got one from Nashbar for like $15. Put the wheels in a padded wheel bag, put the frame in the bike bag, and just carry them in as luggage. If the bike is bagged, then nothing can get dirty. Problem solved. If you don't have a bike bag, use a blue poly tarp and some duct tape to make an "envolope". Tie the flap closed with twine. Again, problem solved.

But at a B&B I'd just leave it in the car. Life's too short to live that paranoid.