I don't think that is the question.  Some foreigners are uncomfortable with the public nudity involved with going to public baths, but I think it's a great, unique Japanese experience.  After the initial awkwardness I found them extremely relaxing. 

An onsen is a public bath with hot and sometimes scalding, natural mineral water. The water is drawn from a natural spring.  It is believed to be very healthy and great for the skin.  It is also very relaxing and therapeutic.

The really nice ones are found outside major cites in a natural setting and are often outdoors.  They have a great view and some can be very expensive.  Most are connected to a ryokan or traditional Japanese hotel.  At these ones you can enjoy a full weekend with a traditional Japanese meal included.

Co-ed onsens do not exist anymore.  I've heard there are still a few out there, but only in the very rural areas or really unique, natural onsens, and sorry men at these one you will not be likely to find any females.

My American co-worker makes an annual trip with his Japanese girlfriend.  They have a secluded, romantic weekend full of relaxing and pampering.  He does not enjoy the public nudity, so he rents the private onsen and these ones can be co-ed.  So if public nudity is not your thing, like many other foreigners in Japan, I recommend looking into the private onsens, you will have to pay a higher price though.

Sento's are also public baths but are found in the cities.  They do not have the natural spring water or the beautiful nature setting.  They are typically indoors.  These are often crowded, but are great for a quick hour trip after a long, hard week.  Sentos are a lot cheaper then an onsen.  They also have many different types of baths.

I have experienced electric baths where a small electric current is sent through the water.  This was a little uncomfortable for me so I wasn't soaking in there too long.  I've also experienced extremely hot baths and then jumping in the ice tub where ice is dropped into the tub at regular intervals.  This was a bit of a rush.  They also have large heat stones that you an fully recline and relax on.

So you now know about the onsen and sento, now for some proper etiquette.   Tattoos are usually forbidden in the public baths.  If you have one make sure it's ok, you don't want to be asked to leave at a later time.  You should bring your own towel, if you forget one they have towels available for purchase.  You are provided a locker or basket sometimes both for your belongings and valuables.

Strip down and stow all your gear, if you want you can bring your towel, and head for the shower.  Next sit down on the little stool and rinse off, if you are really dirty, use the provided soap and shampoo to clean off.  This hot water will also prepare you for the hot tub.  Once your clean hop into the tub.  No rules in here, I've heard you are not to bring the towel into the water, but I've seen many people do it anyway.  Most put the towel to the side or wear on their head.  You can also wear the towel walking around the place if you are not comfortable.

Remember to the Japanese this a very common experience, they have enjoyed this experience from childhood and are comfortable with it.  You will be the only one feeling awkward.  You will get some stares, but only because you're a foreigner, not because they are checking out your "junk."  Just try to enjoy this relaxing experience.  It's one more thing to cross off the list during your stay in Japan.

Don't forget to check out the other articles if you're Newbie in Japan.