A great and true LPSG question! There are a lot of myths and errors which can make it very uncomfortable indeed. To answer your question: Nope, it doesn't hurt for me. Not even on a 100 mile ride. Okay, I'm XL-big and not XXL-big, but I take the liberty anyway to share some experience that can be useful for guys of all sizes.
Fist of all good fitting cycling gear takes away all the chaffing and keeps things snuggly and comfortably in place without squeezing. The padding in the cycling gear also adds to the comfort, with the right size it's supposed to hug you very gently between your legs without any chaffing. Bibs are preferred because they ensure that the gear doesn't move. They lift things slightly up and keep them in place without feeling squashed. In case you don't like to expose your bulge, they also exist as loose shorts with the lycra and padding bits built in, or as undies. But that way you loose some of the advantages, especially if performance is your objective. I point my junk up and it's never in the way that way. Quite a few cyclists do that actually. Note: all this will NOT work if you wear normal lycra or compression shorts. It has to be dedicated cycling gear.
And then I use a custom fit saddle with an opening in the center which takes away the pressure between the legs.
And then, the right position on your bike is super important too. Lots of problems occur from a saddle that's too low, or moved to far forward. Even an inch can make a big difference.
And then, of course, being fit and well trained makes will make things a lot easier too.
Indeed, wearing the right cycling shorts/tights helps a lot, they are supposed to lift the balls and separate them a bit, without feeling squashed. Also, sore balls may be one of the signs that the saddle isn't the right shape and size, and the seating position is wrong, such as too narrow seat area which distributes too much weight to the front, or a saddle positioned too low or too far forward.
Proper saddle fitting is super important when you like to ride a lot. There are all sorts of saddles for different anatomies. This can for example be taken care of by using a saddle with an opening in the center, and the right size in the seating area. Example, you can Google Selle SMP, for which I use a custom fit one. But there are also cheaper brands with make fine saddles with good anatomical features.
Very detailed answer