Personally I think Indian Muslims have integrated in India.
They should be accepted in India.
Here is my thought..
1-Indian Muslims are like regular citizens of India...It is not like they always think like a block.
2- People who stays in cities and exposed to media and education, are definitely suave and like regular Indian and bat for India...But they also resent and protest for the discrimination that they face due to inherent nature of our society..Again, this is to be noted, that discrimination exists in India not for Muslims only, it can be anything like Caste, status, region and so many f** factors which even i hate to list out...
3- Nationalistic Hindus, are anti Pakistani...But nationalistic Muslims are not so anti Pakistan as Hindus...And this is where the clash of perception comes into play..
4- Now, the reason, Indian Muslims are questioned not because they are patriotic, but their priority of religion and country...
5- Hinduism is not so rigid like Islam...So for us, nation comes 1st at the expense of religion...which is always in doubt for Muslims...That creates confusion and question the intetrity of Indian Muslims in the mind of majority..
Most importantly, even if Hindus questioning the patriotism of Indian Muslims does not mean, Indian Muslims are less patriotic rather it is a glarity disparity in perception of how we define our nationalism to our citizens...Being multi cultural society, we could not really strongly define it...And Congress Gov took a short cut of just keeping the problem under carpet for long due to which we have a situation where extreme right wing Gov in place...