IMHO, the seller wants to sell to a buyer without agent, so he can save the commission fee around 6%. The buyer might also be able to negociate a better price b/c of that. For buyer, unless you are experienced, better be safe to go with an agent.
I also heard many agents are not so keen about For sale by Owner houses. The reason I am not sure, I would guess the owner might be harder to deal with than an agent in his trade.