Bangladeshis have been hit hard by the Bodos. The reasons are many -
i. The Bangladeshis so far had immunity. They had full voting rights in India and hence the political parties protected them.
ii. Many of them (if not most) have been declared D voter, meaning they are doubtful voters. Thus they have been constitutionally barred from voting in India.
iii. This is the reason why they lost the protection that the political masters provided them.
iv. The Bodos always wanted to eliminate these Bangladeshis, they were dissuaded because of the political muscle of the Bangladeshis. With that gone, the inevitable has happened.
v. The death toll is much higher, in a short period of time the Bodos would have completed the job, had the army not been deployed swiftly.
vi. This is not exactly a Hindu Muslim or a Christian Muslim conflict. It is a native vs outsider, Indian vs non Indian. But that said, Bodo places of worship (they are polytheists and worship in temples, the type of temple differs from mainstream Hindus though) have been destroyed by the goons of new Islamist parties that have recently mushroomed there. After the armed forces are withdrawn the Bodos will do this again ... and again.
This is as blunt and honest an answer as it can be.