I bought the same bike 3 weeks ago after not riding a bike since I was a teen. It took me about 3 weeks for ass to "toughen up" now that it has, the saddle really doesn't bug me much at all and I've done all my riding in regular shorts, no padded cycling shorts. Give it a couple weeks and perhaps invest in some shorts too.
So far I'm loving the rapid, though i've had some issues with flat tires here in NYC, no fault of the bike tho
FWIW, I'm 245lbs so a little bit heavier than you