I think you should assume that the tour guide is doing their job first and foremost. He probably has scripted responses to questions, at least in part. The guide's response doesn't sound overtly prejudiced. I mean, sometimes Muslims do bad things. Sometimes Christians do bad things. Sometimes, etc. etc. Maybe that's not the best way to approach the topic of tolerance at a museum for tolerance, but based on just that one line I wouldn't assume it meant one thing and I'd want to ask someone to clarify if they did say something like that.
Regarding tolerance as a thing in general. It's good. It's also good to point out where certain things have failings on the whole when necessary. I would say that one should respect people's personal beliefs, but I'm not going to, for instance, be tolerant of extreme religious beliefs, like ones that get people so mad as to shout at and threaten elementary school girls for being hussies*. Those people are showing a great deal of intolerance and I wouldn't tolerate it even if it was their religious belief.
* Not the actual word used. You know what it was.