After years of using a MTB for all types of riding I decided to buy an entry level road bike last year. After the first few rides I considered leaving it to collect dust in the back of the garage and sticking to my MTB. I found that the ride was unbearably harsh, my hands were sore and my lower back ached after 20 miles or so. After doing a little research I decided to persevere and things did get better. Gel mitts sorted out the sore hands and the back pain lessoned as I became used to the drastic change in riding position.
At Xmas I bought a carbon road bike which once again feels different to my other road bike and has created some discomfort at first but once again I believe that this due to a slightly different riding position.
Now my original road bike feels like an old pair of slippers and I could sleep on it.
My conclusion is that bikes are like shoes, they look great in the shop and feel great for the initial try on but once you start using them you need to break them in. I realise that this conclusion isn't very scientific and I would certainly seek expert advice if you feel that things aren't getting any better for you because as already stated there is a lot that can be done to make your riding position more comfortable. But please stick with it the rewards far outweigh the discomfort.