My dealer said don't bother with the automatic car washes -- It's a tight fit, and they degrade your paint over time. They even had a Raptor owner bring one in that went through the wash and left a scratch down the side of the truck (too tight of a fit).
I was told to wash it by hand in the summer, and in the winter take it to a self-wash where you can use the pressure washer and bring your own buckets/towels.
This is especially notable if you have a darker paint, which will lose is luster in automatic washes faster than a lighter paint will.
Oh, and inB4 the "it's just a truck" comments. If you're as OCD as I am, you'll want to wash it by hand.