I mean the philosophies of R&H and punk are almost a complete antithesis. R&H were building on a tradition, not tearing one down, were optimistic, not nihilistic, were obsessed with graft, not raw energy and drive replacing craft, and were bent on creating, not celebrating a post-modern recycling of signs because the future was over.
BUT that's not what Damon meant. He meant they were daring, broke the rules, and presented things you "weren't allowed" to present--from opening with a quiet ballad and no chorus to killing a major character onstage. Yes, the analogy is silly, but it's well-meant, and I think it will be taken and has been taken for what he meant as a connection between the two rather than the myriad ways in which they have no connection whatsoever. I'm sure it's important to him to bridge a culture he loves today with one from long before his birth he fells drawn to now. And it may help some young people give R&H a chance. What's wrong with that?
People have said Mozart was a punk. And I'm sure they've said it about Shakespeare, too. It means "they were revolutionary and they weren't fuddy-duddies in their time, no matter who encased in old-fashioned culture they seem today."