When I got my road bike, I ride 90% of the time in the hoods, and my hands don't hurt. I will move them to the bars or drops perhaps the other 10% just to change position and give them a rest. My handlebars are slightly higher than my saddle. I am not really sitting upright, but I am not leaning forward as aggressively as some other bikes. My Ruby came that way and I just adjusted the seat height.
When I got my Bike Friday which has a straight bar, my hands were killing me after 10 miles. (It didn't bother me on the test ride.) I could tell that the reach of the handlebars was too far away and the handlebars were the same height as my seat. I was putting too much weight on my hands. I was on a trip and miserable. I went to a bike shop and bought an adjustable stem and was able to bring the handlebars to a position that was more comfortable - closer to the position on my Ruby. I think you might need to replace the stem on your bike.
Fit is really important. There is no need to suffer. If you suffer too long, you can damage yourself and then you have to spend all this time recovering from something that should have never happened. Don't tough it out. Riding should be fun.
2007 Ruby Comp/Specialized Dolce
2004 Bike Friday Crusoe/Specialized Dolce