Finally, a question I know something about! Any grounded conductor stuck high in the air is indeed more likely to be hit by lightening than surrounding structure, whereas an un-grounded conductor of modest size (a chimney cap on a masonry stack) is no more likely to be hit than the masonry itself.
As static charge builds in a cloud, the potential (voltage) reaches a point where it can break down air. That potential is a function of distance, which is why tall objects are hit first. A tall insulator cannot dissipate charge, but a tall conductor can, particularly if well connected to ground.
Wood houses are not good conductors, but being covered in water (rain), they're better than air. This is why houses were getting struck by lightening even before the days of electrical wiring. In those cases, the water (and wood) would become superheated by the lightening strike, and the house would be set ablaze. In the late 1700's, partly thanks to our dear old Ben Franklin, they realized a grounded conductor placed high on the roof would make a good target for this lightening (better conductor than the house), and if they carefully routed the wire from that conductor to ground, the charge could be safely dissipated without setting the house on fire.
Fast forward 300 years, and our houses are now filled with miles of wiring, and those old lightening rods are much less necessary. Yes, all this wiring makes houses a better target, but now the strike can be similarly dissipated to our grounding rods or plumbing, with usually no more damage than a few TV's and computers.
Getting back to your question, a metal chimney cap atop a masonry chimney is of no concern. I suspect even all-metal chimneys are not grounded to the structure, and are therefore little more likely than anything else to take a hit. That said, should it take a random hit, I would not want to be touching the metal stove to which it is attached!
This is a very common debate among sailboaters, whether to ground the mast or not. Those who do, argue that it will save the boat from setting fire, should the mast be struck by lightening. Those who don't, argue that grounding the mast will actually make it more likely to be hit. Both arguments are valid.
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