Simple Truth: When your Primary Virtue is 'Tolerance' you cannot see any other Principles as Virtuous.

Illustration:
A man speaks in strong support of monogamous relationships, of waiting until marriage to have sex, and of the virtues of such lifestyle choices.  He speaks of the bad things so often associated with the alternative lifestyle choices- broken relationships, broken families, multi-generational poverty.  Advising people to make the former choices of the latter, he is labelled 'intolerant.'

A man speaks out against practices strongly correlated with institutionalized poverty and lawlessness.  He decries the habit of some young men of wearing their pants around their thighs.  He explains that numerous tattoos and a lack of proper grammar can limit your station in life.  He is labelled 'intolerant.'

Explanation:
When someone sets 'tolerance' up as their primary virtue, it necessarily prevents any other virtue from being virtuous.  To someone who's main virtue is tolerance, courage is not a virtue to be lauded, it is intolerance to be stopped.  In this case, honesty is not a virtue, it is intolerance.  Inasmuch as all virtues are necessarily supportive of some behaviors, neutral towards others, and exclusive of yet others, all virtues are, to greater or lesser extent, intolerant.  Courage does not tolerate cowardice.  Honesty does not tolerate dishonesty.

However, of all the virtues, the pseudo-virtue of 'Tolerance' is the least tolerant of any.  Tolerance cannot remain neutral on any issue.  On every issue, it must make a statement, because all actions, all issues, apply to one or more virtues.  A man who was truly 'Tolerant' of all views could never have an opinion.  Yet there is no such person.

It turns out, in fact, that cries for 'tolerance' are not cries for tolerance at all, but cries of intolerance: intolerance of some other, truer virtue.

Indeed, 'tolerance' is not a virtue at all.  Tolerance is not something one can believe, it is something one has, or does.  We tolerate those things we do not like.  It is not possible to 'tolerate' something with which you disagree, because tolerance, at its heart, is putting up with something that bothers you.  You can tolerate pain, or an annoying voice, or smoking (if you're a non-smoker).  You cannot tolerate happiness, or wealth, or a soothing voice.  These are things people like; they are things that require no tolerance.

Once this misconception is cleared up, it is easy to see that it is not intolerant to speak in favor of one virtue, and against its opposite vice.  Tolerance has nothing to do with our opinions, or our philosophical stances.  I am 'tolerant' of smoking in that I believe it to be gross (you don't 'tolerate' something with which you like) but that I am not going to condemn any given smoker.  If asked about the issue (or, as in this case: as illustration) I will mention that I believe smoking is a disgusting habit.  Tolerance has not entered the picture here, at all.  Tolerance comes in when we get to the question of "what will you do about it."  And the correct 'tolerant' answer is: "nothing." 

I will not go on some anti-smoking crusade, attempting to paint smokers as evil.  I will not claim that cigarette companies are evil.  Neither will I condone smoking, or get terribly upset when a community- as the community, through its city council- decides to ban smoking in public places or restaurants.  Tolerance says I will put up with it when someone chooses to smoke, it doesn't say I have to agree that there is some God-given right to smoke.

This is true of all issues.  All issues have some relation to one or more virtues or opinions.  Virtues and opinions are, by their nature exclusive.  Therefore, to have an opinion, or to uphold a virtue is 'intolerant' to some degree.