Though one understands that majority of muslims are patriotic, but it is a fact that some (either Indian or Pakistan / Bangladesh)Muslims are behind such terrorist activites in the country, that to for the cause of a foriegn country(Pakistan). If after such incidences Muslims are looked with suspicion to carry out the investigations, it is not unnatural.
If Muslims wish to avoid such situations, they have to be proactive and cooperative to report activities which they feel is suspiciously carried out in their locality.