The FFRF was not set up as an "atheism organisation" but to defend the separation of church and state as set out in the First Amendment in the US Constitution. This may be why you were not aware of them. Most of their activities revolved around banning prayer in public (i.e. state) schools or displays of the Ten Commandments in government buildings and other things like that.
Thus the FFRF had a focused mission and is not explicitly atheist. After all many theists also agree with the separation of church and state and those that do not often think it should only be their church that enjoys the approval of the state.
Of course, you are correct about mission creep and, as so often, the people who push for it tend to be atheists with a non theistic ideological agenda.
I wasn't aware of them either - but if they are US-based, then that wouldn't be unexpected.
But I think you are right - even from their name, it seems to me that their focus would be secular rather than atheist. And those are not the same at all.
And in a broader sense I think it is important to distinguish between the following:
Atheism (or theism) - simply a belief or lack of belief in god/gods, which comes with no further agenda, particularly if you are talking about a lack of belief.
Secularism - which is, effectively, a political position about how a jurisdiction should operate politically. And there is no reason why a commitment to secularism should necessarily align with atheism. As JP points out there are plenty of theists who are committed to secularism.
Moral (rather than political) philosophical positions, e.g. humanism. Again distinct from both of the above as plenty of people may consider this to be a specifically personal position rather than something that should be adopted as an official, or political, position. And humanism is not the exclusive domain of atheists - indeed humanism grew from religious positions which ultimately determined that it was preferable to have a moral position that did not rely on god, rather than considering that god did not exist.
So although the three often align, e.g. with people who are atheist, secular in political outlook and humanist in a personal philosophical position, they are not interchangeable. And you can also map these onto theistic positions - where being a theist simply means a belief in the existence of god or gods, but does not require any religious commitment. Religions themselves often adopt both political positions and also moral philosophical ones.
