You might have a 100 complaints about muslims and their religion, but such discrimination in the name of religion should never be tolerated. Such discrimination only succeeds in further alienating a community that already feels alienated. In the US they have the concept of "equal housing opportunity", which makes it is illegal for apartment owners to discriminate in the name of race, religion, ethnicity, sexual orientation etc. In the US the emphasis is "assimilation". In India the emphasis is on "tolerance". Maybe we have things to learn from the US here.
A point to note for my muslim readers though. We (hindus) hear about all the extremism going on in the name of islam. In the west, one can do a background check and credit check based on your social security number. It's hard for someone to know your background in India because there is no such concept. People rely on word of mouth and generally tend to trust their own kind. I'm sure muslims have the same prejudices about hindus.
I guess in time we will make our peace with each other. Till then we all need to keep trying.