This is a two-way street. There are plenty of people out there who see Muslims as the enemy, and they have their own motivations for feeling that way. "Islamophobia", which is the popular catch phrase these days, is by and large a product of the very mentality you pointed to. That many Muslims have no allegiance to the Western nations they inhabit, and will use terrorism as long as their own political beliefs aren't adhered to. That is not a phenomenon that instills much trust between the non-Muslim and Muslim communities.

As to your overall point, it does have merit. Western governments should be more mindful of the changing dynamics inside their countries. When issues arise involving Muslim peoples abroad, they should be more careful as to how they address it and what policies they embrace. However, that doesn't mean Western governments should feel obligated to cater to Muslim political sensibilities at every turn. Especially under threat of terrorist activities.