I think there has to be a middle ground. I wouldn't want to be around a guy who continously lets foul-smelling farts and thinks its cute. On the other hand, I think one can be overly prudish. I work in health care, so I smell other people's shit all the time--it's part of the package we call life.
If two people are in a relationship, have seen each other's naked bodies, fucked, eaten each other's asses and ingested their cum, that's about as intimate as it gets. If you plan to live together for any length of time, you'll have to live with each other's quirks, and bodily functions are part of that.
Having said that, I know how embarassing it can be to come out of a bathroom after stinking it up. I think the best advice on this comes from married couples, who were also prudish about farts, etc., early on and years later don't really give a shit (no pun intended).