It will get easier, but make sure your bike is adjusted correctly. If it's not currently, then changing the seat height, handlebars, and seat angle will make a world of difference to your comfort.

I ride with a messenger bag. I put about 30 to 35 lbs in it most days. work clothes, tools, lunch, coffee thermos, milk for my coffee, u-lock, lights and battery incase I get stuck at work late. wallet, phone, ipod, keys. It all adds up. And I ride a brooks saddle, un padded. I'm just saying, that so long as your bike is adjusted properly, the weight on your shoulders should not hurt your tush any more than just riding without that extra weight.

but...if you're sore then taking an extra day or 2 off, to let things heal and toughen, may be a good idea too.

But make sure your saddle is adjusted right. if it's too low, it is very hard on your knees, and I think it actually puts more pressure on your rear then, as you will find it harder to push on the pedals (which would take the weight off your rear). If your seat is too high, you will be rocking your hips as you pedal, and that will cause rubbing. if your seat is tilted at the wrong angle, it will put pressure on the wrong points, making the ride uncomfortable, usually an almost level to slightly downard pointed seat is comfortale for most people and applications.