I get that all the time. I usually interpret it on the energy that is in the place. I think places hold on to memories of what happened there. So if you are sensitive, then you will pick up the stronger memories a place holds. It makes sense that you would get a bad feeling a certain parts of a church, especially given what happened to so many young boys in churches. Also many times when people go to church it is to pray when thing are not going well in their lives, so those memories and feelings are absored into the room.
It can also be recent events too. Like you walk into a room full of people and immediately get a vibe of happiness, anxiety, pain, fear, etc. Or you walk into an empty room that was just occupied and the feelings of what happened are still lingering.
As Mark said, you don't have to run out of a room, nothing will hurt you. You're just one of the lucky who can pick up the feelings. Do you work on developing these abilities Spider Rob?
True and good Point