No, "half the country" did not even vote. Significantly less than half the popular vote was for Trump.
The final election results were Clinton 65,844,610 Trump 62,979,636 If you call the difference significant (2.2%), then what does that make the gross value of 62 million americans that might be turned off by his rant?
Even if this were a strictly cynical action on Colbert's part (and I don't think it is) you could make the argument that given Trump's unpopularity you might create more value out of bashing him than you lose from his supporters.
Moreover, I suspect that Colbert's target demographics skew richer, younger, and urban/suburban so he probably has less to lose and more to gain by alienating Trump supporters anyway.