I think it has something to do with the fact that your home AC's compressor runs on electricty while your car's AC compressor is driven by the engine.
Your home AC's compressor is basically a large motor. Motors draw huge amounts of current when they are starting (upto 10 times the running current). That's why you may notice that the bulbs in your house dim slightly for a fraction of a second when the compressor starts up. The 3 minutes waiting is probably to give the compressor's motor windings time to cool off, since it might get quite hot with that huge starting current.
In your car, the worst thing that the AC can do by switching on / off often is increase the wear on the belt & clutch mechanism of the compressor but even with this, the compressor in your car would probably outlive the car itself !
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