Freedom of Speech my ass!
There is freedom of speech/expression and there is calling for muslims to be terrorists. Freedom to criticize is one thing to incite violence is another. There IS a difference.
Firstly, the implications of calling for muslims to be "terrorists" isn't as black and white as you imagine, because it all depends and what he means by terrorist (and if you read the context in which he said it, it is all the more ambiguous). I think you'd find it very hard to win a prosecutation of Mr Naik on incitement grounds.
Secondly, by your logic, the Apartheid government in South Africa had every right to persecute Nelson Mandela, since he supported terrorism, and incited South Africans to become terrorists.
Thirdly, also by your logic, a great many media outlets in the West would be banned (the majority in anglo-saxon countries), since they all caled for and supported the war in Iraq.
Now muslims are complaining that everyone thinks they're terrorists but how many of them complain about these "scholars" who say they should be terrorists?
You're talking about Muslims as if they are one homogenous group all with identical opinions. I think you might find that different Muslims complain about people thinking they're terrorists, compared to the Muslims that have wet dreams about Mr Naik.
Now what if I was one of these "scholars" and say that, "all non-muslims should be terrorists because a policeman is a terrorist to a robber therefore all non-muslims should be terrorists? How would you feel as a muslim? Should I say, "suck it up, I have freedom of speech?"
Right, so it's a race to the bottom, with the bottom being Islamic morality? Good luck mate