As someone who considers myself a very liberal lefty tolerant sort, I do think in the UK we have a real problem where some people bend over backwards to be tolerant to everything, to the extent that they tolerate intolerance.
It's okay to say that certain values and behaviours aren't acceptable in a modern civilised society, and to openly criticise them.
It is okay to say that men and women are equal, and it's not acceptable to pressure women to cover themselves to avoid tempting men.
It's okay to say that beheading someone because they have shown an image of a religious figure is in no way acceptable.
I even noticed people criticising the staff at Charlie Hebdo for the cartoon they published of prophet mohamed, because it 'incited violence'.
I think everyone has a right to view religious beliefs and actions with a critical eye, and everyone has a right to say they don't want their child exposed to certain beliefs being portrayed in a positive light.
And yes, every religion has its problems. The answer isn't to say you can't criticise any. The answer is to pay more attention.
I'd be amazed if the school visits to different places of worship involve balanced and nuanced discussion about people's beliefs and what's good and bad about them. Unfortunately I'd be concerned that every visit would paint the religion as being positive and all beliefs and actions worthy of respect under the name of religion. I'd be astounded if after the mosque visit the teacher leads a discussion on why women are expected to cover themselves in Islam, or why Catholics opposed abortion or why fundamentalist christianity doesn't accept gay marriage, and so forth.