A simple "no" would do, rather than telling someone to change how they feel about being naked in public.In this case a "simple no" would suffice, but we would be letting the OP down if we don't try to encourage her have this cultural experience.
kat,
Yes, we know you may be uncomfortable being naked with other people, but the onsen is not some nudist camp pool party, rather its usually a quite reserved place where people go to relax. Generally speaking, no one will stare, and you should be somewhat covered by your towel when out of the water, and covered by the water when in the baths. You should try to build up the courage to experience this if you feel you can, and if not there are spa resorts where you can wear swimsuit. Just know that these are not onsen and it is not the same experience.
This is not me imposing my values on you, rather encouragement to open up to a cultural experience. But I also agree that if you really feel uncomfortable being naked in public, then you may not want to visit the onsen as it a place to be naked. If you don't think you can enjoy it then why go? Thats a valid suggestion.