Here is a new post at EconLog in which Bryan Caplan discusses how signalling contributes to the status quo bias.
The lesson: In the real world, signaling naturally tends to ossify behavior - to lock in whatever the status quo happens to be. If you're an optimist, you can protest, "It's only a tendency." But even an optimist should admit that this tendency leads to atypically slow and unreliable progress.
Most intolerance doesn't announce itself. It usually dresses itself up as something positive.
The cynic in me would say the so-called tolerant people within our society aren't actually tolerant, rather they've adopted a potpourri of non-traditional behaviours in order to signal their faux tolerance, and then act with intolerance to so-called traditionalists (who are racist, homophobic, misogynist, authoritarian, etc). It all depends on how you value the liberal project. Personally I think it rests on shaky foundations, so I have some sympathy for this cynical view, although I think there are genuine moral concerns caught up in a very confused (and often destructive) ideology.
Probably the strongest example of intolerance dressed up as tolerance, though, is Western political ideology and how we relate to other societies. The democratic countries are extremely intolerant of other political systems; probably more so than many of their most hated rivals. This is expressed in terms of freedom, individual rights, etc, but elections and other Western political institutions are only tenuously connected to freedom. It's certainly not the case, as is usually assumed by Westerners, that elections are by definition a form of freedom and no further argument is needed. A case needs to be made.
Most discussion of Western political ideology tends to assume what it's trying to prove. For example, it's assumed that being incarcerated for a political crime is much worse than being incarcerated for something recognised as a crime in the West, but this is only obviously the case if you already agree with Western political ideology. It's not hard to come up with arguments (the standard line being that it's too easy to abuse) but if a country started giving political prisoners fair trials and following accepted legal practice for incarcerating people based on well-defined political crimes, would we accept that? I doubt it. The fact is that we won't accept anything short of them adopting our practices because their perceived superiority stems not from the particular benefits of adopting them but from that they are ours.
The same is true for freedom of speech, assembly, etc. I've been stuck in traffic because of a protest and it occurred to me then that marching down the street is something we make an exception for in political circumstances but would almost definitely outlaw if we didn't have that ideal. Are countries that don't share our ideals outlawing protests because they hate freedom or because that's just a really, extremely obvious thing to outlaw if you don't share our ideals? Calls for elections in countries without them are calls for the destruction of the prevailing political system. In the West, communists, fascists, anarchists and other rivals to the prevailing political system (as opposed to a party within the system) are not tolerated either. They're often demonised and sometimes they're arrested.
These are some of the ways we disguise intolerance for political and cultural differences as sympathy for the plight of individuals under other regimes (while simultaneously ignoring their differences from us, as if everybody has a Westerner trapped inside them, just waiting to be freed). There's also the tendency to file under propaganda any expression of political views that doesn't fall under the party system (for example., that the party system is not optimal). There are Chinese and Singaporean political thinkers (and some leaders) who write very eloquently about the limitations of Western political thought and are summarily dismissed as having ulterior motives. Almost everything the Chinese government does is dismissed as a way to prop up the regime, as if nobody there cares about the fate of their own country at all.
Of course, this all stems from the Western idea that the state is an antagonist and opportunist rather than an organic part of society (and, relatedly, that society doesn't transcend the individual). These ideas are not shared by others but, again, rather than provide an argument we just assume differences in opinion are examples of oppression. Often these differences in opinion are shared by the very people we consider "oppressed" (this is where we bring in nice words like "enlightened" which deny the autonomy of the individual we're expressing our sympathy for; once they've become like us, they'll understand why being like us is better, but until then... well, screw their opinions).
I think it would be interesting to analyze in more detail what you mean by "intolerance". We might distinguish the sort of "intolerance" that is expressed by mass violence against its target, and the sort that is expressed by simply not taking the target's claims very seriously.