Hundreds of billions of dollars in revenue and an unprecedented leap to the top of the list of most valuable companies in the world seems like pretty good compensation already, no?
No, he just means that Apple would have been well-rewarded by its innovation even if it hadn't been granted the patents in question, ergo, it wasn't necessary to grant the patents to encourage innovation.
Patents should not be granted willy-nilly, and especially not on broad 'implementations' that essentially cover the whole concept, because then it just turns into a huge land grab.
I'm already wondering if I should attempt to patent any half-cool idea I implement on my site, even though the idea of it stinks to me. With the way doubtful patents appear to be less spurious than expected, I'd be remiss not to grab my share of the land where I could. That's a crappy state of affairs, to have to attempt to patent everything that moves.