Because no matter how big or capable of self publishing you think you are, steam is bigger and more capable.
The initial sales of Elite relied heavily on the Elite brand name, so FD could afford to sell it on their own at first without sacrificing profit via Steam, as they knew there were many people aware of the game already and ready to buy it asap no matter what, even at the cost of losing the convenience of the Steam environment.
It's been 3 months since release now, and most of those who knew about the game probably made their decision already, so it was time for Frontier to tap into this huge reservoir that is the Steam playerbase, of which a sizeable portion possibly never heard of the game. Whereas only those people interested in the space genre and from a certain age knew about the game back in December, the steam release exposed the game to the quasi entire PC playerbase. Regardless of how much of a share of the profits Steam will take per title, FD will certainly make it back several times due to the increased volume in sales. FD and the Elite franchise aren't so big that they can indefinitely ignore Steam if they want to keep selling copies.