According to Chamber's 21st Century Dictionary:
adjective: (often intolerant of something) refusing or unwilling to accept ideas, beliefs, behaviour, etc different from one’s own.
[18c: from Latin intolerans, from tolerare to endure.]"
Put simply, you do not have to accept the beliefs of others in anyway in order to be respectful of their right to believe whatever they wish. You certainly do not have to agree with another individual's views in order to support and defend their rights. Being intolerant has taken on a number of meaning that the actual defintion does not support.
If theists want to verbally attack non-theist for not buying into their bullshit they can but that does not give them any moral higher ground. In fact, what it really does is expose their own ignorance and hypocrisy. They not do not understand the terminology they choose to make use of they do not apply it to themselves.
Note: I will admit that on occasion I have made the same mistake. I try to catch myself but I do sometimes slip.