Choosing to ignore the various "FoT is here now and it's good so 2238 will die because it's rubbish and it smells" comments previously (I don't think any of them came from any FoT devs), I doubt the intention was malicious. You can understand why someone would want a little confirmation before investing months and years of their life into developing a project - nobody wants to work their arses off for several years for free, only to have their project suddenly closed.
Anyway, to my knowledge the FOnline stuff has always been "sort of fine" based on the fact it's technically a mod - you need to own the original (almost 15 year old) game to run it, though it happens to run those assets through a completely new engine. Obviously it's always been a slightly grey area - but shouldn't be considered to be less legal than any of the older mods on NMA, including those as simple as adding or adjusting a sprite, or even the tools such as dat extractors and frm viewers.
Anyone involved in the original Fallouts must have been interviewed on NMA about 10,000 times each by now, so it's probably fair to assume that they were aware of other mods including FOnline, and haven't made a complaint yet. Of course Bethesda might see it differently as they a) still exist as a company, b) are actively promoting other games from that license and c) have different aims and values.
The thing with the poster guy could be seen as worrying, but two notable parts were that the web address had the full word "Fallout" in it, which could be seen as "confusion about branding" (perhaps "fallout-fan-art-posters.com would have been okay?) and that it had so much attention - over 100,000 downloads. By comparison, FOnline is more like a hobby for a few hundred people.
If they get a positive response or no response, then that's a good thing - it stops being a grey area and becomes "officially okay", though a negative response might lead to a lot of urgent design work for "Post Explosion Nuclear Isometric Simulator 2238".
Worryingly, if they get through this bit, you do wonder if such problems will reappear if/when an offical Fallout MMORPG is released.
