I made a proposal to someone to settle an issue and he answered "fair enough"
I assumed that he agreed to my proposal but does this expression imply that he wasn't very happy with my proposal or does it simply mean a neutral "ok" in that context (business)?
He did agree to your proposal, yes. Whenever I say "fair enough," it doesn't necessarily mean that I don't like what the other person proposes, but moreso that I begrudgingly accept to make a compromise over my original argument/opinion.
While it may not be a "neutral ok," it turned out to be acceptable to them, so I doubt you have anything to worry about.
(not a teacher, just a language lover)