The article says they are theoretically only arming groups that are fighting against ISIS. I'm pretty sure if they can defeat them on the ground without committing American troops (airstrikes can only do so much) and only spending $1 billion dollars they are going to consider that a big win.
The sentiment of this question explains why even further. ISIS does very bad stuff and is a major problem, and we can all wonder why the west doesn't do more to stop them because they clearly have the ability to do so. But then the moment the US gets really involved, everyone is going to shift blame to them for everything. I don't condone secretive actions like this myself, but considering the US's global influence and capability, if they weren't doing something about ISIS the question could easily be restated "What does the US government gain by allowing extremists to rape and pillage the middle east?"