Preventing this kind of confusion is the entire point of Trademark law, and whether the company's name did this intentionally or not, I think Moot has a reasonable cause for concern and case.
I personally think moot is very much descriptive of the 'discussion' in general. Moot, the 4chan creator would most probably argue the name has acquired distinctiveness through usage but this generally requires a high evidential threshold in terms of the reasonable person having familiarity with the term as a unique identifier. Whilst if 4chan had been called moot from the start he would have had a stronger case, I do not think the reasonable internet user would be aware of moot's name let alone identify it with online discussion.
There is quite a strong case I think. Moot is the online brand of a person who runs one of the most popular forums on the internet. Starting a forum service with his name is quite clearly in a grey area if not outright infringement.
However the main reason why there will be not be a long drawn out battle is because there are likely to be no damages and moot.it are unlikely to have any real assets.
I think it's fair to say that a large majority of internet users would have no idea of the founder of 4chan. Plus the term is being used in a descriptive allusive sense from what I can tell. A firm rebuttal is in order.