If you have an old or non-supportive saddle, it could be that it needs replacing...however, a good quality seat won't really "look" cushy or padded. The Terry company makes lots of nice seats especially designed for women, or your local bike store will have plenty of options (and should be able to tell you if there is anything wrong with your seat, but be careful of people that just want to make a sale).
The most effective thing you can do is get good quality biking shorts. Yes, if you haven't worn them before (and been around rides where everyone else does), they may seem to look a little funny...tight lycra with very obvious padding in the crotch and halfway up the backside. However, they really work, and everyone DOES wear them. Black is usually the most flattering and minimizing color. Be sure to get ones recommended for comfort and distance, not Tri-shorts or spin shorts...those may look "cuter" due to their shorter length and much thinner padding, but that's exactly why you DON'T want them for road bike rides of any significant time/distance. If you are very self-conscious, they do make some with matching "skirt" coverups, either as a separate piece that you can put on when you're not on the bike, or as one unit. The skirts that are intended for riding look restrictive to me, but I've never tried them.
Your comfort, health, and safety are the most important things...get good shorts! (The padding in the shorts also often have an antimicrobial feature...remember that bike shorts are meant to be worn without an underwear layer, which could cause chafing at the seams as well as defeat the antimicrobial purpose).
(many online sources...Team Estrogen, Terry, bikesomewhere.com, etc, just do a search on women's bicycle apparel...or a local store of course).
My current favorite shorts are made by Sugoi.