The root cause of this problem is the division of India on linguistic basis. In just 60 years (for a nation 60 years is too small a period) these problems have started.
While, one can rightly say that the methods adopted for these protests are wrong, it must be noted that Karnataka has always got a raw deal from the Centre. The locals were overlooked for jobs in Central services and PSUs, where Tamils have been filled in. This obviously hurts the locals. The water issue gives an opportunity to vent such feelings.
It is very nice for all to say that we should have feeling of one nation. But, then the Govt should also show that we belong to one nation. They should ensure equality to the locals (infact preference if they may).