When I flew the CRJ, company policy dictated that the CA & FO's bags went over row 10 on the -200. I heard of only one incident where a pilot's bag went missing after being put in the overhead. Anything which is possible is inevitable. As stated above, never put anything you can't live without in your bag. Plenty of room for your laptop up front with you.
If I was in a rush to get off the plane to make a tight commute home, I'd put my rollaboard up front, but other than that I found it to be way too much hassle. The risk factor is low, take reasonable precautions, but don't worry much about sticking it in the back with the cattle.
Even when you're flying out of Philly.
