That is strange, I have a 2001 hyundai elantra GT -black with the exact same problem. It is especially bad on the hood but it is also on the roof. Looking at it carefully I believe it is corosion under the paint, They probably don't have a good paint primer. to fix this problem you would have to sand all the paint and primer off down to bare medal, and then put a good primer on. I know that would be so expensive the car is not worth it.
I am going to the hyundai dealer to see if they are going to do anything about this, If not, I will never buy another hyundai. My car has 59,500 miles on it.
What good is the 10 year - 100,000 mile warranty if your car looks like a piece of junk!