Virtue is a good habit which participates in reason, which is the principle of good actions, of which no one can make bad use, which God works in us, without us. This is the definition of virtue that one can derive from St. Thomas Aquinas' Summa Theologiae I-II.55.4c. It is derived from St. Augustine's definition of virtue, found in De Libero Arbitrio ii, 19. (Properly speaking, of course, this is the definition of infused virtues, of which God is the efficient cause, but if we remove the phrase, "which God works in us, without us," then it is true of all virtues, both infused and acquired.1)
The habit of tolerance, as it seems to be defined today, is the habit of taking a permissive attitude towards evil. By a permissive attitude is meant a disposition which allows that which one is disposed towards to happen without interference or protest. As to what this permissive attitude is directed towards, it cannot be the good. This is because the good is that which is desired and sought out, not what is simply allowed. That this permissive attitude is directed towards evil follows necessarily.2
This should be sufficient to show that tolerance is not a virtue. A virtue is the principle of good actions. But tolerance is the principle of not acting against some evil. But to not act against evil that one has a duty to act against is to do evil. Thus tolerance can be the principle of doing evil and so cannot be a virtue.3
1. Technically speaking, God is the efficient cause of all virtues on the metaphysical level, since habits are beings, if only per accidens. But on the physical level we are the cause of acquired virtues, while God is the cause of infused virtues. See St. Thomas' reply to objection 6 in the above mentioned article.
2. Some would argue that since we are primarily talking about a permissive attitude towards actions there is the option of neutral in addition to good and evil. I disagree. Actions, like habits, are beings, if only per accidens. An action either posses the fullness of being that an action should posses, or it does not posses said fullness of being because of some defect in form (the object of the action, what John Paul II calls the proximate end in Veritatis Splendor), accidents (the circumstances of the action) or cause (the intention of the agent, what St. Thomas calls the end and what John Paul II calls the remote end in in Veritatis Splendor). Thus, an action is either good or bad. It seems to me that acts which many call neutral are ones which either posses only a small degree of being in their fullness or have only a slight defect.
3. It is true that individual acts of toleration may not be evil. It would not be evil to tolerate the evil of the law allowing a criminal to avoid punishment, since an individual citizen does not have the authority to act in the place of the state in such a situation unless the state has deputized him to do so. In general, an act of toleration is a good thing when you do not have the authority to stop the evil or when acting or openly protesting against the evil would result in greater evil and disorder than refraining from acting or openly protesting the evil would. But the virtues that would govern these individual acts of toleration would be justice--which would govern whether or not you have the authority to act--and prudence--which would govern whether or not acting would lead to a greater evil than not acting.