When you install anchor bolts, you should drill the holes all the way through the slab. When it is time to get rid of the anchors, you simply remove the nut and drive the entire assembly down flush with the slab or all the way through the slab if you like.
Thanks, all, for the suggestions. It took a while because I moved airports, but I ended up installing bolts following Kyle's suggestion.
My previous airport (Cedar Rapids) has high standards for maintenance, and they required that I petition to modify the hangar in any way. I did, and they said I could drill the holes after they had the utilities marked, so long as I either remove the bolts or drive them in flush when I vacate, to avoid tripping hazards.
For unrelated reasons, I then moved to another airport before I drilled anything. At my new airport they weren't so picky. They informally approved my request to drill with no special requirements, but I felt that it would be best to follow the good practices that the previous airport required. So I followed Kyle's suggestion to drill through all six inches of concrete -- that way the bolts can be hammered in flush, years from now, when I vacate.
I used a common kind of bolt like this:
It is about 6" long, and I drove it into the hole in the concrete so that it protrudes out of the floor by about 3", which is plenty for the 2 by 4 boards that the winch is mounted on.
Jim asked why such a big bolt as 1/2" and proposed that a much smaller bolt would be okay. I agree -- that's because pulling a plane up a one-degree incline requires less than 100 pounds of force, which isn't going to shear a smaller bolt. However, I was given a winch for free -- and it already had a bracket for 1/2 inch bolts. It isn't that hard to drill a 1/2" hole through 6" of concrete, anyway -- it takes just a couple of minutes while leaning gently on the hammer drill.