I purchased a used bicycle and the seat that came with it was awful!  As @roadtrip said previously, "Most often, the larger softer bike seats cause more issues . . . " <-- very true!

I got this saddle (link & image below) from REI and it's a fantastic upgrade - it was inexpensive and was very easy to install.  I can put 20 to 30 miles on my bike (my average ride distance) and have zero pain.  However - if your bottom is not conditioned to bicycle riding, and you go out for several miles, then you're probably going to experience discomfort regardless of the quality and correct fit of the bicycle.  

Tips that might help:  move forward/backward a little bit while riding - stand up occasionally - take a break and get off the bike for a while.  It's my guess, from zero riding to "reasonably conditioned bottom" will take at least a couple or three weeks of riding with frequency.  If you are riding on a regular basis, you have a decent saddle, and your bike is setup (fitted) properly, then after a while, your bottom discomfort will no longer be an issue.

 

saddle, 01.jpg