The NBA is a business, and their business is entertainment. Pop sitting four of his top five scorers, including all three of his stars, in a nationally televised game against a top opponent, is clearly bad for business. I can't blame Stern at all for punishing the Spurs for that.
I think it's Pop's prerogative to strategically rest his key guys, but resting them all at once in a game against a good team (rather than against a team like, say, the Magic, who the Spurs played in their previous game), is kind of a slap in the face to the league office.
I'm not saying a penalty (fine or otherwise) is a bad thing but I will say that MANY top tier teams rest players... to start penalizing the Spurs is STUPID. If you don't like them doing it, say so before the season starts, be clear that no one can "rest" players! You can't just single out Spurs and not penalize others. When Doc rests KG, PP, and RR (or any of the guys), as a fan, it doesn't bother me because I am smart enough to know that there is a larger plan in motion... I also enjoy when they sit (every now and then), so I can get a look at other guys who may turn out to be a missing element (Avery got that shot when Ray was out)... you may need one of the "scrubs" to stand up one day and help win games, they won't get any play when there are 10 guys that have proven themselves, ahead of them.