In our private lives, when we claim to merely "tolerate" something, we mean that we "put up" with it. We allow it to happen but we do not necessarily approve of it and feel under no obligation to refrain from criticism. Thus, I may "tolerate" the fact that an adult child smokes, but I do not hesitate to tell him that I disapprove.
The meaning of tolerance in public life, however, has moved beyond simply letting something be to include the notion that tolerance of a person or an idea means acknowleging that she or it is "just as good as" anyone or anything else - or at least refraining from criticism. Thus, if I oppose criminalization of homosexuality, but nevertheless condemn it as "sinful" I am said to be "intolerant."
This kind of tolerance is bound to crack-up in the end as the controversy over the Danish cartoons depicting Mohammed demonstrates. It cracks up because it eventually requires us to approve of the intolerant. If tolerance toward Islam means that we must not criticize it, then how do we respond when Islam itself becomes intolerant as Muslims around the world have over these silly cartoons? If we must pretend that Islam is everywhere and always a "religion of peace" while much of the Muslim world is interested in anything but peace, then how do we respond when the Muslim world acts to undercut the very idea of tolerance that prevents us from speaking uncomfortable truths?
What we wind up doing is validating the demand for the supression of speech. CNN refuses to show the offending cartoons. An editor of the French paper who ran them gets fired. Bill Clinton likens the cartoons to anti-semitism. Who is not going to think long and hard before running anything like this in the future?
We wind up with civil peace, I suppose. At least for a while. But we get it on the terms of the intolerant. In the end, they shut us up.