By way of various experiments, I have cooncluded this to be a not just 1 thing causing it, but a combo of many things, which if you get them all wrong, will cause you a lot of discomfort...
- Saddle choice.
- Saddle position.
- Padded shorts.
- Pre-ride chamois cream.
Saddle choice is critical, get it wrong and you definately should not be spending anymore time riding uncomfortably, and should change it immediately. For me, being fairly heavy at 100kg+, a Fizik Aliante VSX (Bull) saddle was the widest and firmest option with the biggest channel down the middle and made the biggest difference straight away.
Getting the correct saddle to take the weight of your sit bones is the biggest factor, then once you get that right, you will find you only have minor discomforts to deal with, and that is where saddle positioning (Fore/aft/tilt) all come into play, so again this will require experimenting, which for me were the weekly 2hr club rides.. Immediately after each ride, whilst still "fresh" from the saddle, work out which part is sore, and adjust the saddle tilt by never more than 5mm at the absolute most...
After a few weeks of messing until that was spot on, got some decent shorts (Endura 260 pro) with wide ass pads, but was advised to go down 1 size to make sure they were tight and didnt move around, and DAMN what a difference, its like night/day...
Decent chamois cream is good too, so long as you have the first 3 items sorted. If you get those wrong, chamois cream isnt going to do a great deal for your sore ass