It's a cultural thing. Every time I go see the parents in PR I have to contend with it. As far as PR is concerned, it began in the 80s as airlines really became more commonplace down there. For most people in the island who haven't flown before, getting on an airliner was a big deal. More contemporarily, it's mostly comprised of the "we're going to Disney" crowd. Transplants from the island (such as myself) usually treat it with mild neglect, as it's all really an indication of lack of cultural exposure. Sometimes it's hard to avoid though. The transplant crowd is not really guilty of the clapping offence anymore, except for certain "domiciles", most notably MIA, MCO, and JFK (newyoricans...never been to the island but clap anyway, what the f$ck they clapping for? LOL).
You want the full experience? Fly MIA-SJU, MCO-SJU, JFK-SJU, particularly through AA, and holy sh%t brother get ready for it. I'm back living in the south now, and I much rather fly ATL-SJU non-stop on DAL than do the "macarena" on ATL-MIA(MCO)-SJU on AA. Close you'll ever get to flying SWA to the caribbean if ya ask me..If Southwest ever starts serving SJU, I'm hoping a Carnival cruise to get there. Yikes! lol