Because they realized he was a disaster, both for the country and the Republican party.
Despite their lionization of businessmen, Republicans believed that presidents should have some political experience. Many of them also recognized Trump as a failed businessman who was only rich because he was born rich. (Marco Rubio famously, and accurately, said that it Trump hadn't been born rich he would be selling knock off watches on a street corner). Most Republicans also recognized that Trump was deeply deeply ignorant and even more stupid and that he lacked the temperament to even be a functioning adult, much less run the country.
They also recognized that he'd be a disaster for the GOP. They figured, incorrectly as it turns out, that 2016 would be a bloodbath for them if Trump was the nominee. But they may have just been off about the year. 2018 was a bloodbath for Republicans and 2020 looks like it won't be great either. If Clinton had won, the GOP probably would have kept the House and made even larger gains in the Senate. The savvier Republicans also recognize that Trump will be absolutely disastrous for them going forward. Two thirds of Millennial voters voted against Trump in 2016. If that number holds true for Republicans as a whole then the 2020s and 2030s are going to be bleak years for Republicans. Trump is tying the Republican party ever more closely to unpopular ideologies and faltering demographics. In particular he's made white supremacy the centerpiece of Republican ideology at precisely the time when whites are becoming less of the American population. To survive and thrive going forward the GOP can't rely on just white votes. But Trump makes it essentially impossible for them to appeal to other races.
Republicans also recognized that Trump didn't believe in a lot of the things they believed in. Trump wants low taxes, but not out of any philosophical conviction that taxes are wrong, but rather just because he's greedy. Trump doesn't believe in the free market. He doesn't believe, interestingly enough, in American greatness. And he positively rejects Christianity and its morals. So they were concerned that Trump wouldn't advance their interests.