This article is misleading, in that the fee boost is not just for Denali, but for "17 parks nationwide."  Perhaps the article should have named those parks.  It is true, though, that Denali only allows driving as far as Savage, whereas the un-named other parks may allow driving all through the roaded sections of their parks, which would comprise more miles of road, making it seem unfair to charge vehicles so much at Denali.  
Also, this fee increase experiment may be occurring under Zinke, but it is unfair to attribute it solely to the new administration.  Do I like increased fees? No, especially since there are a lot of other services in or near parks that cost money. However, the problem of maintenance backlog is real, no matter what administration runs things. What I really worry about is involvement of private corporations in funding public park services, something we may see more of as time goes by.