The food was fairly good....
It's rather hot in here....
Fairly indicates something less than completely positive - better than "so-so", but less than "very" or "quite" (I'm talking U.S. English here).
Rather indicates something more than "fairly".
"He is a rather good singer" (Positive - quite good)
"He is a fairly good singer" (Less than completely positive - above average, but could be better)
While the meanings overlap to a degree, there is a difference. Some native English speakers don't know them.