It's a right 'o passage. Once they harden up, you'll be able to make cleaner chords. I find that if I don't play for even a few days, I can feel them softening.
Also, as others have said, your guitar setup plays a big part. I found once my strings were lowered, that I could play barre chords easier and cleaner. Well worth the money.
Sore/painful fingers
What everyone says is true. Do your daily Finger Aerobics and once your finger strength is built-up you can play all night. You might also check that you are not applying more pressure to your strings then is necessary to achieve a clean sound.