Rajnikant did the right thing by apologizing to the people of Karnataka for any hurt feelings that may have arisen due to his Hogenakkal speech. There is no point in having property damaged across the Tamil Nadu and Karnataka and have the lives and properties of ethnic Tamilians and Kannadigas endangered. We are all Indians first. Rajnikant is probably most acutely aware of that fact, being an ethnic Maharashtrian that worked in Karnataka and then achieved fame in Tamil Nadu and Andhra Pradesh. Life is too precious to be sacrificed over a silly movie.
Plus the film is loosely based on Sudama and Krishna. So Krishna has to protect and not cause damage. Ofcourse a Tamilian who has lived most of his life in Tamil Nadu or a Kannadiga living in Karnataka would be either angry or gleeful as they have never been outside the well of their own state.
Actually it is nice to see some Tamilian anger; they have been worshipping filmstars blindly for too long and have been robbed silly in the process. The maximum prosperity that they achieved was possibly under the guidance of a non film star politician, Shri Kamaraj. The film star politicians and their minions have simply filled up their own tummies.
Plus Rajnikant was against the goondas that did property damage; he never said anything about Kannadigas in his original speech. The apology was the weapon that he used against the same goondas so that they do not get the opportunity to tarnish the image of Kannadigas even further.