In fact, it takes real confidence to show tolerance. Moses could have been threatened by the prophesies of Eldad and Medad, but in confidence he let them go. Jesus could have worried that there were those using his name to heal without authorization, but in confidence he tolerated them. Paul could have condemned those who preached Christ out of selfish ambition, but he had confidence in the proclamation of Christ even from wrong motives. Tolerance is a better way.
Tolerance is a better way because intolerance is ineffective.
It does nothing but damage to the cause it seeks to defend. Attack a heretic, and you give him an audience. Banish a book, and everybody reads it. Condemn a sin, and some want to try it out. An intolerant attitude will alienate the sinner rather than draw them to a loving, life-transforming God.