There has never been any doubt that his father was a full-fledged, card-carrying member of the GOP establishment.
And a former CIA director.
And of course during the Bush vs. Kerry campaign, it was pretty much a choice between Bonesman A and Bonesman B.
Here’s a “left field” theory:
The people around Bush felt that McCain was “more dangerous” than Obama (mainly in the area of foreign policy). It could also be that the GOPe was terrified of what Sarah Palin might do to them, esp. if McCain kicked the bucket after a year or two.