Q:

Why is rudeness tolerated?

I've noticed a few posters on serverfault that take potshots (ad hominem, or insinuations of stupidity) at people.  This would seem to be in violation of:

Always be polite and have fun
  It’s fine to disagree and express concern, but please be civil. There’s a real human being on the other end of that network connection, however misguided they may appear to be. We’re here to learn from our peers, not yell at each other.

However they seem to get away with it.  Is it because they have high rep, or because they hang out with mods in the chat rooms?

A:

If you were looking for an actual answer to:

However they seem to get away with it. Is it because they have high
  rep, or because they hang out with mods in the chat rooms?

First, you should have posted examples, but according to your comment you keep thinking certain people are excluded from the rules and are part of the "in crowd clique".
As MarkHenderson and Voretaq both have explained, no one is "above the law" here.  If the citations were valid the offending party, regardless of rank/file, would be dealt with appropriately.
However, just like with Amex, membership has its privileges.  One of those being that if the person was judged offensive and had high rep they would probably be told "you know better" and that'd be the end of it, typically.  It is different if the user is new and simply starts posting insinuations of stupidity as you call it.
This is no different than our personal lives.  Your siblings can mess with you more than a complete stranger can, with mom and dad only telling your sister "stop picking on your brother" whereas they might really let a stranger have it.
It also depends on the seriousness of the post.  Again citations would help here.  Offcolor/personal insults aren't tolerated, period.
You also have to bear in mind that context/intent is very hard to convey online and often taken however the reader wants it to be taken.  The "offending party" might not even realize they were being offensive.  The reader might simply be having a bad day and read into something that was never really there.
This is also why there is a "flag" available so that mods can look at someone's post and help determine its merit.  If it still doesn't get the attention you think it deserves that's where citing the post/comment here in Meta is appropriate, and beyond that going straight to the SE staff via the "Contact Us" link.
Hope that helps.

