http://mw1.m-w.com/dictionary/tolerance definition "2 a: sympathy or indulgence for beliefs or practices differing from or conflicting with one's own "
I personally like the Church of Jesus Christ of Latter-Day Saints' recent discussion on tolerance in respect to the subject of gay marriages:
Tolerance, Same-Sex Marriage and Religious Freedom
Those who favor homosexual marriage contend that “tolerance” demands that they be given the same right to marry as heterosexual couples. But this appeal for “tolerance” advocates a very different meaning and outcome than that word has meant throughout most of American history and a different meaning than is found in the gospel of Jesus Christ. The Savior taught a much higher concept, that of love. “Love thy neighbor,” He admonished.  Jesus loved the sinner even while decrying the sin, as evidenced in the case of the woman taken in adultery: treating her kindly, but exhorting her to “sin no more.”  Tolerance as a gospel principle means love and forgiveness of one another, not “tolerating” transgression.
In today’s secular world, the idea of tolerance has come to mean something entirely different. Instead of love, it has come to mean condone – acceptance of wrongful behavior as the price of friendship. Jesus taught that we love and care for one another without condoning transgression. But today’s politically palatable definition insists that unless one accepts the sin he does not tolerate the sinner.
As Elder Dallin H. Oaks has explained,
Tolerance obviously requires a non-contentious manner of relating toward one another’s differences. But tolerance does not require abandoning one’s standards or one’s opinions on political or public policy choices. Tolerance is a way of reacting to diversity, not a command to insulate it from examination.  The Church does not condone abusive treatment of others and encourages its members to treat all people with respect. However, speaking out against practices with which the Church disagrees on moral grounds – including same-sex marriage – does not constitute abuse or the frequently misused term “hate speech.” We can express genuine love and friendship for the homosexual family member or friend without accepting the practice of homosexuality or any re-definition of marriage.
There are those who claim that religious or morally motivated individuals are intolerant because they do not accept a course of action or activity because it clashes with thier values. In reality they won't consider a person tolerant until they are accepting or condoning of the activity with no value judgement whatsoever.
I really like this video on tolerance: