Why? They pilot the ship. They're pilots.
Also as pointed out before they're been occasionally referred to as pilots since the TNG era shows. Though usually in reference to shuttles, not the starship.
This rebranding of 'helmsman' to 'pilot' has been subject to creep since TNG, and then exacerbated by Voyager and Enterprise, as well as First Contact. Roddenberry used to talk about Trek being 'Hornblower in space' among other things, evoking imagery of slow, graceful moving sailing ships. Hence the use of the term 'helmsman', which also has modern naval roots.
Then you see the episodes like "The First Duty" and "Chain of Command", which emphasize more traditional 'flying' skills more in line with aviation. (Riker being the only 'pilot' on board capable of flying that mission) In first contact, the flight of the Phoenix was very much a 'test flight' akin to Yeager breaking the sound barrier. Zephram Cochrane becomes not just the 'inventor' of warp drive, but the first warp drive test pilot, as well. Then there is Tom Paris aka Nick Lacarno aka Captain Proton. Helmsman? Yes. Pilot? Very much so. I think more than anyone else, Paris's character was the first true overlap of the two.
With Mayweather they return to the terminology of 'helmsman', but you still have Archer and his background as a 'test pilot' along with A.G. Robinson, once again pushing the limits of the 'warp barrier' in a program reminiscent of "The Right Stuff" and Edwards AFB back in the 1950's and 60's. Mayweather, and all other starship helmsmen and shuttle pilots, by extension, are 'pilots'.
So I think this is something of a natural evolution, and one I am okay with. I think the USN has rebranded its submarine helmsmen (planesmen?) as 'pilots', but I was an aviator, not a sub officer, so I'm not 100% sure on that. In modern Trek, the way we've seen the ships maneuver (much more like aircraft than sailing ships), I think the term 'pilot' is more appropriate, especially given that the ship's 'pilots' like Ortegas also get assigned to fly the smaller craft like shuttles. Which isn't to say that someone like Spock or the Scotty couldn't do it, but it isn't their specialization, and they would rely much more on AI computer assist and control.