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.
As a result, the fiercest opposition to Trump comes from the sorts of people who value those ideas the most: writers, intellectuals, veterans of past Republican administrations who have implemented them. Rare among elected officials, Ryan came to Congress from that policy-driven world, having worked at a think tank as a disciple of the late conservative hero Jack Kemp.
Intraparty opposition isn't nearly as strong among Republicans most interested in counting votes. Senate Majority Leader Mitch McConnell, for example, has made his reputation as tactician above all. Once Trump emerged as the presumptive Republican nominee more than a week ago, McConnell decided that a quick, if unenthusiastic, endorsement was the smart play. Trump's ideas represented a smaller barrier for him than Ryan.
Of course, both men have to count votes to keep their leadership jobs. If Democrats gain five Senate seats this fall, Charles Schumer will replace McConnell as majority leader. Seven Republican-held seats are up for election in states President Barack Obama carried twice. McConnell will encourage vulnerable members to take whatever stance toward Trump they believe will help them win.
Democrats need to gain 30 House seats to allow Nancy Pelosi to reclaim the Speaker's gavel from Ryan. That's a much more difficult hurdle than they face in the Senate. Because of how congressional boundaries are drawn, most incumbents hold relatively safe seats. Trump's success during the primary in many of those safe districts represents a source of pressure on Ryan to fall in line behind the nominee.
At the same time, there are several dozen districts in which Trump could heighten the vulnerability of Republican candidates. Many of them include large numbers of Hispanic, Asian and college-educated voters Trump has alienated. The plight of Republicans in those districts represents a source of pressure on Ryan to hold back and prevent House Republicans from being too closely identified with Trump.
There's one other source of pressure on Ryan to hold back. Republicans with an eye on future elections fear that demographic changes leave the party with no choice but to expand their appeal with nonwhite voters. They fear Trump has made that more difficult.
Among those Republicans looking to future elections: Paul Ryan, potential presidential candidate in 2020.