The most important reason is simple. Ryan cares about policies and ideas more than most politicians do.
There's a pattern to opposition to Trump within the GOP. It's strongest among those motivated by the policies and ideas that characterize the modern conservative movement: limited government, low taxes and free markets.
On key flashpoints of the 2016 debate, Trump doesn't share those ideas. He opposes major trade deals backed by past Republican presidents. He vows to resist curbing benefits for the Social Security and Medicare programs headed for long-term insolvency. He backs a wall on the border with Mexico and the deportation of 12 million illegal immigrants already in the U.S., who have come to represent a substantial segment of the American labor market.