Dougherty agrees with a lot of the positions Donald Trump has taken, but he didn't trust Trump to be up to the job. He was also convinced Trump would lose by a large margin. He wasn't alone in any of that. Dougherty hasn't written for the Atlantic for several years.
I was in the same boat when Trump first declared his candidacy, and he still says and does things that I find troubling, but it didn't take me long to stop and say, "Wait. Who else do we have? Trump isn't necessarily the best messenger, but at least there's someone out there getting the right message out." I supported Trump because no other candidate was talking about immigration and national sovereignty, and I think Dougherty should have done the same instead of breaking bread with NeverTrumpers in the establishment (such as praising Cruz's failure to endorse Trump at the GOP convention).
As for his concern that Trump would lose, it seems to me that the right message is the right message, whether it wins the election or not. It's true that Trump won by narrow margins in the swing states that carried him through and the outcome came as a surprise to me, but bad poll numbers aren't a good reason to abandon a candidate.
I still read Dougherty's op-eds sometimes because he's a decent writer and has good things to say. For all his flaws, I still prefer him to the trash that you get from National Review or the Weekly Standard.