We have always used Walmarts and Cracker Barrels, as well as other areas for an overnight when going on a trip of more than one day. We always go in and do some shopping and ask permission when at a business.
Years ago, we went to a Life on Wheels seminar the week before the PA RV show. There we attended a seminar on RV safety. They offered many tips on insuring your safety when parked. Here's a few of the tips they offered that we have adopted. I always keep a 2,000,000 candlepower spotlight, a boaters hand held air horn, and a can of bear spray by the door. A bright light in the face at night will sure make one pause. An air horn blast also makes anyone approaching pause. The bear spray is the last resort. Thankfully, I have never had to use any of these.
About the worst disturbance we have encountered is the cleaning service running a street sweeper around the Walmart parking lot at 3:00AM in the morning.
We just got back from ME, VT, NH, NY and CT. The majority of our stops were in campgrounds, but while traveling, we overnighted at at a CT RV rest area, Cabela's, Walmart, and a NY Throughway rest area. At all locations, we felt perfectly safe.