I think it's a combination of a few factors.
First, there's a sort of ethical code among some fansubbers that dictates that they fansub for "the love of anime" or something to that effect, and that it's improprietous to profit off of fansubbing. I'm not sure how effective a reminder of this sort would be to people who don't subscribe to the same ethical code (i.e. the people at whom this message would be targeted), but there you have it. Sticking a reminder on your fansubs is pretty much a no-cost endeavor, so it's not like it can hurt.
Then, there's the belief that explicitly stating that you do not intend to profit off of your fansubs makes you less liable for copyright infringement. I doubt this has been tested (I don't know of any litigation against fansubbers), but I rather doubt this would be of much value as a legal defense - statutory damages (as opposed to actual damages) are available in USA copyright infringement cases under federal law (and, I imagine, in other jurisdictions as well).
I suspect (but have no evidence) that this is a holdover from the pre-Internet days of fansub distribution when you actually needed to pass around video tapes to get your anime fix. Exchanging physical materials is likely to get you more scrutiny from law enforcement than exchanging digital information, and this relates to my previous point: infringing copyright is bad, but profiting off of infringed copyrights is probably worse, or at least that's the general perception. C. Griffin's answer to this question contains an interesting view on the matter, from the perspective of someone who consumed fansubs in pre-internet times.
Adam Davis also brought up in a comment another point I meant to address - fansubbers don't want other people profiting off of their work - it's kind of a slap in the face. So what's one way to do that? Stick a big "this is not for sale" warning on it, kind of like how a lot of free (gratis) software comes with a notice saying something like "if you paid for this, you should ask for your money back because this is free software".
So here's the problem: basically all fansubbing these days is done with "softsubs" - that is, the subtitles are basically a text file that accompanies a video. It's dead easy to edit these things (particularly using software like Aegisub), so this is probably another reason that you don't see these disclaimers anymore: they're easy to remove. In the pre-softsub days (maybe before 2008~2010 or so? I don't have my chronology down for this very well), subtitling was done by re-encoding the video to have the subtitles ("hardsubs") baked into the video file. Since this is much more difficult to alter, disclaimers would have been more permanent (and hence, useful) back then.
Anyway, I haven't seen a disclaimer of this sort on any fansubs from at least the past five years or so - it's gone the way of the dinosaurs. In the modern fansubbing world, where all exchange of fansubs is electronic and hardsubs are obsolete, these disclaimers serve no actual purpose.
(I have seen this sort of thing on recent manga scanlations, though - but that's a topic for another question. The key difference here, I suspect, is that scanlations are still "hardsubbed", so to speak.)