It is true that instinct drives a great deal of human relationships and interactive behaviors with the opposite sex. In fact it is this very thing that I believe makes guys not want their girl fucking around. The "Alpha Male" mentality or what have you.
Besides all that though, here are some other reasons why a guy wouldn't want his girl sleeping around on him. Anybody can add to this list if they want, and I believe these are pretty reasonable, logical things to believe in.
1. Diseases - Perhaps one of the most obvious. Of course you have to accept your girl has probably been with guys before you, but even then you can go get tested together or something to that affect. If she is sleeping around she probably doesn't want to raise extra suspicion by risking a trip to the local clinic for a little scrape test. So in short I would rather not have to guess where these spots on my dick, or my tongue are coming from.
2. Mental Health - It has not been proven whether or not human beings are "instinctively" monogamous. Once you really settle down with someone, it is supposed to be because you have found someone you are supposed to be happy with, if you are not happy with this person then break up with them, and then go sleep around. At least it would show some courtesy instead of making them into a cuckold.
3. Mental Healthx2 - If you are in a relationship with a girl, and you two are having sex, as most women would expect that if you have sexual urges that is what they are there for. If you have a girl who is cheating on you, now you have to wonder what she is looking for elsewhere that you aren't giving her. Whether it be a bigger penis, better look, better oral skills what have you. You now are left with whatever feeling of inadequacy you believe (or are told) caused her to cheat on you.
4. Respect amongst peers - Whatever the reasons she is cheating on you for, once word gets out (and it will, maybe even before you hear about it because that is the nature of the beast) others who know you are going to question why. Now given the society we are in the man is blamed if he is cheating outright, but if a girl is cheating it must be because of something the man is not giving her. Thus his social standing amongst his peers, and as a potential mate for other females who know about it, is significantly lowered.
If I missed any, anyone can feel free to add to it.