Why would you ever feel that?
It is open-source, and has contributed alot to the community. In my eyes, Gateway has too, but its nice to see things being opensource.
Gateway has been all about running games. With Smealum's Ninjhax, he might just have kickstarted a nice homebrew scene (by delivering a full homebrew launcher solution). There was no homebrew apps before and Gateway didnt give a crap about it - now they do and now there is homebrew apps
Also, it might still be useful having paid for (if that is your only concern, and not the actual practical use of Ninjhax). I can imagine that Gateway will not add homebrew launcher compability immediately, so it might be your only shot at running homebrew for a while
(Atleast the one compatible with Ninjhax).
...You can also run homebrew on 2 3DS' now maybe
(that is nice, if you are going to buy a N3DS - buying another Gateway would cost dollars compared to just buying Cubic Ninja
)