That is certainly a problem. In the UK at any rate, even most of the practicing Christians tend to be very liberal in their interpretation of their faith. There are very, very few Bible literalist/creationist types. And most of them would describe themselves as tolerant of other faiths, Islam included. But what they really mean is that they expect Muslims to of a similar liberal stripe to themselves, the sort that maybe have a copy of the Qu'ran in the house, but probably don't attend the mosque, do wear western clothes, etc. - what I call "C of E Muslims".
But seeing women covered from head to toe, work colleagues needing areas where they can pray several times a day, and so on, runs massively counter to the secularising trend of the last fifty or even hundred years. They are uncomfortable with it. Frankly, I am too; I find it deeply depressing.
Three flights from NYC to Tel Aviv within the last two months have been delayed from takeoff, one as long as 12 hours because Hasidic men refused to sit next to women. Incredible. They should have been arrested on the spot. If they were Muslim, I bet they would have been. If you want to live in a Western country, you must adhere to it's laws and norms. If you refuse to do so on religious grounds, you should either be deported (if you have dual citizenship) or fined and jailed.
That's what makes yesterday's massacre so egregious. It was an affront to core Western values of freedom of the press and free speech. If the killers are French citizens, it is doubly distressing, because they will have completely rejected those basic values in favor of a stupid fairy tale.