I see so many intolerant groups of people promoting tolerance, it's become a bit of a joke to me.

What is tolerance to you? If you promote tolerance, you promote tolerance for everyone, regardless of their beliefs, even if their beliefs are intolerant. I constantly hear this out of the LGBT/Feminist movements in particular, where the only form of tolerance being pushed for is tolerance for them. Very often, these people promoting tolerance suggest that it should be illegal to disagree with them. It's dumbfounding to me, so I'm wondering if people's concept of tolerance differs.

One of my favorite arguments for the form of tolerance I suggest is this, John Locke's "A Letter Concerning Tolerance", which concerns an issue similar to many plaguing our society, a couple hundreds of years ago which was solved relatively amicably.

So, again, what is tolerance and to who does it apply? If it doesn't apply to everyone, what is the precedence for intolerance towards a group?

Tolerance is an idea fed to the masses to curb tensions between groups that are inherently different. Weaker groups hide behind it, the dominant one rebels against it. It's the product of liberalism, and it's needed because of rampant multiculturalism and egalitarianism.

In autocratic states, dissenting groups get silenced with lead. In democratic ones, you let them do whatever, and feed them rhetoric with ideas of tolerance and equality when you need their vote for the next term.

For what's the precedence of intolerance, it's just what happens if nobody's around to tell people what to do.
If you move into an all-white neighbourhood as a black person and get somebody from that same neighbourhood fired from his job because you can do it for cheap and more effectively, you'll get crosses burned on your lawn and dudes in ghost costumes flailing their pitchforks at you. Human nature 101.