It seems to me that while many fears are irrational that many are legitimate and real enough, rooted in facts. The difficulty is a matter of sorting these from the irrational ones. Fear seems to be about as biological a function as any. "The organism" wants to protect itself from harm. Perfectly natural.
A lot of psychology--or psychotherapy--seems to be about the process of learning how to distinguish between those fears which are an accurate and honest assesment of genuine threats and those which aren't terribly reasonable. The latter, it appears, tend to result from two factors: social conditioning and trauma. These, unfortunately, don't appear to be all that separate. For example, I was traumatized sexually-emotionally by growing up a queer boy in a queer-hating society. I'm well along the path of recovery from this truama, but it would have been much better if I could have been comfortably and honestly (and openly) myself from an early age.
Sadly, this does not bode well for our society's antipathy toward non-monogamy, whether homo- or hetero.