To be truly tolerant, yes, sometimes we do have to simply accept people saying or writing whatever they please.   I agree, sometimes it is not easy.  I disagree with several things on these comments sections, but I do not respond to all.   
As far as your example is concerned, yes, you were intolerant.  This is not necessarily a bad thing.  I do not know all the context around your example to say whether or not it was good for you to do what you did.  A more tolerant action might have been to let him have his say, but coming back with where you disagreed with him.
Also, remember 1 thing about me, I grew up and spent most of my life in the Olympia and Seattle areas.  This means that, as a conservative, I have had to learn to have some tolerance of views that are different than mine.   This is also true living in the Eugene area.