//Nearly half voted to remain - this was not a mandate for a hard brexit.//
And more than half voted to leave. There was no question on the paper about "hard" or "soft" Brexit. And in any case, the term are meaningless. You're either in or you're out, and we're out. In any case, done that, been there, got the T-shirt.
//If brexit is done, why does the government want to renegotiate the NI protocol?//
Because if you read the protocol it is contingent upon both sides acting pragmatically and responsibly. Unfortunately, the EU has not acted in Good Faith with regards the border issues. The idea was that goods destined to remain in NI would be treated differently to those which may cross the Irish border. That is blatantly not the case: although only 0.5% of goods entering the EU do so across the Irish Sea, more than 20% of all customs checks are carried out there. Hence the need to invoke Article 16 if necessary.