Not necessarily villains, no. In a battle between royalty, every side can be viewed as evil, depending upon who you serve under. However, generally, the Lannisters were seen as the evil of the battle-field, yes, and it was likely the aim of the author to goad the reader into disliking them as well.

Which is of course the house that Joffrey served - and therefor ruled - under. Generally cruel and ruthless, to the point Joffrey refused to show mercy to his lady's father, had him beheaded, had his head mounted upon a stake and forced her to then look upon his head to warn her about traitorous ways.

Despite this, though, I'm rather fond of the character Tyrion Lannister however. Intelligent, witty, and quite amusing.