Mostly, they stand out of respect, a respect as individual as the person standing. Abdul-Rauf's failure to stand was disrespectful to the fans who had paid, and paid well, to see him play. Being from New York, I have attended many hockey games where the visiting team was from Canada. At all of those games, the anthems from both countries were played. All of the players and most, if not all, of the fans stood for both songs.
People stand out of respect for another.
Watch the Olympics this summer. People will stand for other countries when the medals are handed out simply because they respect the efforts of the athletes. It has nothing to do with religion or freedom of speech. Abdul-Rauf should show the fans the respect they deserve. It's the least he can do for the amount of money that he earns playing a game.