It's true that Muslims in Canada are being treated like most new ethnic groups to Canada have been treated (marginalized and stereotyped with pressure to assimilate to wider mainstream Canadian culture). There are some noteworthy differences though:
a) The internet. In the past marginalization and discrimination happened off the grid, now it's there for everybody to see - magnified, distorted and manipulated (politicized) - which makes discrimination against Muslims seem 'exceptional' when really it isn't. This is the effect of the internet/social media on perception, it's similar to the effect on perception with regards to violent crime or any other social ills.
b) The internet/air travel. In the past, immigrant groups coming to Canada had no option but to sever most ties to the homeland and this motivated them to integrate. Today, it is possible to maintain greater familial, cultural and economic attachment to the homeland due to technology, which means the disenfranchised can reach out more readily beyond their adopted homeland when looking for a sense of community or acceptance. This is a double-edged sword, as we are seeing.
c) Current social context in Canada. Canada today is an extremely liberal and tolerant nation, with an ethos that directly contradicts that of many non-western nations (i.e. role of women, gender equality, democracy, growing secularism etc). Previous groups of immigrants have evolved with Canada in this way, to one degree or another, whereas latter groups of immigrants (and certain Muslim groups specifically in this case) have arrived while this process was already complete. This has created a stronger cultural clash than many previous groups had to deal with.
d) Current political/foreign policy context in Canada. I can't think of too many examples where immigrant groups have come to Canada from homelands that had active and explicit political, economic or ideological conflict with prevailing Canadian policy. I'm sure there were some but the point is that Canada is currently seen as a threat and an enemy to many of the nations where recent Muslim immigrants have come from. This has created a stronger conflict of interest than many previous groups had to deal with. *I thought about the Italians, Germans and Japanese during WWII but the difference being those groups were already quite well established in Canada when those conflicts arose.
In the end, the experience of Muslims in Canada is both exceptional and unexceptional at the same time, and is probably more a reflection of the differing Canadian context they have arrived in than a reflection on them themselves.