Well, that's a phase everyone MUST go through... It's to make your fingers stronger which are by nature much weaker for the amount of pressure needed to play the barres. Also, the left fingers are the lesser used ones for a usual right-handed person and that only worsens the situation.
You might even somehow be able to play the 6th string root chords (F, Fm etc) more easily than the 5th string root ones (Bb, Bm etc)... that too is normal cuz the latter does indeed involve a lot more strength.
The only way is to push through this stage - this is what makes the difference between those who stop at the simple chords (which are really very few) thus limiting their further progress with the instrument, and those who are on their way to become genuine guitar players. The moment you'll begin to want to play some of your more favourite songs which are also musically complex, you'll run into these chords that can never be done unless your fingers have been strengthened.
It helps to have a low action on your guitar while learning these (although I learned on the world's most horribly set guitar). And it helps to persist through the pain. I know no other way.
I think it also helps to listen to what the musician-philosopher Jamie Andreas of GuitarPrinciples.com has to say about barre chords:
Here are a lot more informative essays, most of which were referred to in the above ones:
Many times I've lied, many times I've listened
Many times I've wondered how much there is to know...
Mellow is the man who knows what he's been missing
Many many men can't see the open road...
Many is a word that only leaves you guessing
Guessing 'bout a thing you really ought to know...