Ross Douthat is a remnant of the old Republican Party. He is an intellectual who has used his platform on the NYT to defend conservative principles that once defined his political party. Jeff Flake's decision not to fight against a Trump inspired primary challenge bothered him for two reasons. Flake embraced all of the conservative ideals that Douthat has supported durng his career but he concluded that Republicans in Arizona would not vote for a candidate that was critical of Trump. The other reason for Douthat's disappointment was that Flake decided to "die in the dark". He believes that Republicans should not defiantly retire like Flake and Bob Coker. Nor should they cravenly collaborate with Donald Trump. The battle over the soul of the Republican Party should be fought in the light of a political campaign. That would be better than dying in the dark as members of the British House of Lords decided to do in 1911 when it gave up the privilege of veto power over bills passed in the House of Commons.
Flake and Coker chose to resign because they understand the battle for the soul of the Republican Party. The deck is stacked against conservative idealists. For example, Steve Bannon is leading the Great American Alliance to purge establishment Republicans from the party. Trump's campaign slogan was to "Make America Great Again". It is not a coincidence that the name of his alliance resembles Trump's campaign slogan. Bannon's organization is promoting primary candidates to run against Republican incumbents who are critical of Trump. He is joined in this battle by alt-right organizations and media outlets which share his vision of Trumpism. He is also supported by the Mercer family which is willing to share some of its billions to anoint Trump as the Czar of the Republican Party.
The battle for control of the Republican Party is not ideological. It centers on emotion more than it does about political policies. Trump continues to attack Obama and Hillary Clinton for a good reason. His base shares a strong dislike for the Democratic Party. Affective polarization is one of his weapons. Loyalty to Trump as a person, and building hatred in his base against Democrats, is the foundation of Trumpism. Some might argue that Trump's focus on his base will cause more traditional Republicans to leave the party. Some might become independents but they won't vote for independent candidates or for Democrats. John McCain selected Shara Palin as his Vice President candidate when he won the Republican nomination for president. He chose Palin because most of the Republicans, that are now part of Trump's base, have an emotional attachment to her. Palin's support in the Republican Party has never dropped below 67% despite her absence from government.
The Republican leadership in Congress does not like being attacked by Trump or by Bannon. However, they are more likely to "die in the dark" and to collaborate with Trump while he and Bannon complete the takeover the Republican Party. After all, they may be able to pass a tax bill that benefits their large contributors with Trump in the White House. The Koch Brothers are already spending millions against Democratic senators who face re-election in 2018. The Koch Brother ads assume that Trump's tax policies will create jobs and raise wages just as Trump has falsely proclaimed. Their ads claim that the Democratic candidate opposes job creation and wage growth.
Trump's takeover of the Republican Party is the first step in his effort to establish a more autocratic form of government in the US. He has not experience running an organization over which he does not have complete control. After he gains complete control of the Republican Party he will be better prepared to rid himself of the institutions that have been put in place to constrain presidential power.