Yes, they are bumpy; this is mostly a function of the tire pressure (higher = bumpier) though other aspects of design (frame geometry &c) cannot be excluded.
That said, it sounds to me it's your riding style, rather than the bike, that's causing your discomfort. When I ride, I typically have a lot of weight on my arms/hands, and a lot of weight on the pedals. Of course the saddle gets a lot of weight as well, and indeed almost all of it sometimes, but not for extended periods of time. When I go over bumps, I usually see them before I get there and lift myself up on my legs so I have no weight on the saddle when I actually hit a bump. Padding on the saddle does not add comfort, the way I ride. Padding interferes with blood circulation and adds discomfort, at least the way I ride.
I keep saying 'the way I ride' because I am being careful to speak for myself only here. Well, I know there will be plenty of people on this forum who agree with me, because they ride more or less the same way as I; but also plenty who don't, because they ride differently.
Free Spirits are pretty low end, as was mentioned (though the top end Free Spirits aren't bad at all), but I don't really think that's the reason you're experiencing this discomfort.
Mountain bikes are not, in my opinion, comfortable. And don't get me started on suspension!
