If you have gutter mounts (i.e. old fashioned) it's pretty hard to steal a LOCKED roof rack - you have to destroy the gutter to do so.
For aero mounts (flat foot plus a "clip") it's reasonably easy to stand on the car, pull on the bars, and lift the whole rack. It takes a minute or so to do this, less if you have someone prying the clips on the side while you're pulling on the top.
Since the thieves don't really care about the condition of your car, they're not thinking about leaving you with a pristine roofline or attached gutters. Once you get over that mental hurdle, you realize how easy it is to steal a roof rack.
If you aren't using it for a while, remove it.
If you're parking in a rest stop or other high traffic area, park where people can see it. Bonus if you can see it yourself (sitting in the McDs or whatever).
For quick and simple lock methods, use nylock nuts (stainless would be good). Replace all nuts supplied with the rack and mounts with ss nylock nuts You need a ratcheting wrench of some kind to tighten/loosen it, and as a bonus you won't have to worry as much about losing a mount or a fork or whatever as you drive down the road. Secondary bonus, if you are a "racker" (one that leaves a rack on year round), at least the nut won't be rust-fused to the bolt.
Use the locking clips for the aero feet. Beats having someone walk up, unscrew the 4 nut things, and walking away with your rack. At least make them stand on your roof and earn it.
And I'll repeat - remove the rack when you don't need it. It takes 10 minutes tops to mount a rack for the third time if you have two people. The first 2 times I'll give you the benefit of the doubt - it takes a while, esp the first time.
I personally haven't had a rack stolen from me, but one of the cars I own used to be owned by a friend who raced. He had two racks stolen off the car, once while he helped a friend unload bikes after a race. He was helping rolling bikes into the guy's apartment, walked out, rack gone. The roof still reverberates because whoever stole the rack stood on the roof and broke all the welds between the sheetmetal and the crossbeams.
Fortunately the trim things where the clips clipped were relatively unhurt.
I'll use a roof rack if forced to do so. But I prefer to put my bikes inside my car. Saves gas, keeps the bike dry, no chance of losing the bike or a wheel, less stress when making pit stops. I'm into stress-free, and I hate stressing.
Heck, it can even save you a ticket if you drive like it's a crit on the highway. A friend got pulled over once - cop simply followed his bike and tagged him in the middle of relatively heavy traffic. "How did you know it was me?" "I clocked the bike on your roof" "Doh"
If we're traveling long distances with luggage and, say, the tandem, or 3 or 4 bikes, then I begrudgingly concede and we put on our rack and however many mounts we need (2 on there by default).
cdr