We have stayed overnight at rest areas, Flying J's, etc. but we usually prefer Super Walmarts to be honest with you. They're open all night (usually). When we arrive (usually 9pm-midnight) we go in, make sure it's OK to park there, pick up supplies we need and usually our breakfast pastries for the next morning. We usually drop a minimum of $35-$50. I've never felt "unsafe" in the locations we've selected. We usually look & plan for locations that are well outside of any major cities.
We don't deploy slides and I leave our toad in neutral so IF I had to make a quick exit, I just turn the key on the moho and leave. But that's never happened.
Oh, when we arrive, we also make sure to walk the dogs and put the "Beware of Dog" signs in the windows. They're not big dogs (40 lbs.), but I believe they make a would-be ill-doer think twice.
But I have to agree with many of those above. If you can't feel comfortable in those situations, then you should probably just avoid them.
Good Luck & Safe Travels!
~Rick