Road bikes are very different from MTB's. As you ride it more, you'll find it more comfortable because you'll gradually become more flexible and get used to the pressure points.

It is possible that you don't have your seat adjusted quite right. If it's tilted a couple degrees the wrong way or if it's too far back/forward by a few mm, it will be much less comfortable. Also, bike shorts vary a great deal in the type and amount of padding they have. The gel shorts are a bit heavy, but they may be the ticket for you