I have to chime in here!
This is (apparently!) a pretty common problem.
My gyn suggested switching to an antibacterial soap life Safeguard. Definitely helps. But overall, I find it best kept under control by treating it like acne. In most cases, the cysts really are just deep-seated acne. A few things that work for me...
Of course, go commando. I think we all agree on that!
Get out of your shorts asap after your ride
Wear clean shorts every ride (what a good excuse to go buy more bicycling clothes!)
Shower (or otherwise!) asap after your ride and use an antibacterial soap
Use acne lotion such as Proactive with Benzoil Peroxide (sp?) or salicylic acid
Stay away from balms, lubes, gels and bag-balm! Nothing worse for clogging pores! (Really, being a farm girl, I'm a big fan of bag balm, but it's mostly petroleum jelly!)
"No hour of life is wasted that is spent in the saddle" -Winston Churchill