So what do you think? Is monogamy/pairing off unnatural? Was it invented by jealous guys who couldn't get any because alpha males like King Solomon kept all the women to themselves?
Because human children take a long time and lots of effort to rear, monogamy is an extremely useful tool (at least for females), and probably evolved in humans for this reason. However, taking a "gene's-eye" view, it's in the reproductive interests of the male to have sex as often as possible with as many females as possible. The same is not true of the female due to her long gestation period. This is essentially why men cheat when they get the chance. It takes very little effort and there's a chance of passing on their genes with no further effort required. Women who will inevitably have to look after any children they conceive tend to be more choosy and tend to have illicit sex with "alpha males" only while they're ovulating, leaving their nice, dependable husband to look after another man's children.
For atheists, your basis for morality is collective self interest, right?
No, individual rights are the basis of my morality.
Does monogamy serve this interest? Or does it cause weak genes to be passed on?
As people generally pair up with someone roughly on their level, 10s with 10s, 9s with 9s etc., the genes passed on by monogamous relationships are usually about as good as we should expect. But of course selection pressure makes us try to treat the system, to mix our genes with someone "out of our league". The most common ways of doing this are described briefly above.
It seems that our natural state is to be mostly monogamous, but to take chances to maximise the quality and/or quantity of our reproductive potential.
For more information, I highly recommend Jared Diamond's excellent book Why is Sex Fun?