Let me try and translate.
Fighter BOB is 4th lvl and has a strength of 12 and dex of 17
Fighter BOB is fighting with a rapier in his right hand, and a large shield in his left. His current BAB is +4. If he took Weapon Finesse, he would get a +3 for his dex, but a -2 armour penalty for the shield in his left hand. BAB +5.
Now, different scenario
Fighter BOB is fighting dual weapons, he has a rapier in his right hand and a dagger in this left. He has the feats, so he has a (modified) BAB of +2. He takes Weapon Finesse, so he gets a +3; does he get a -X for having the dagger in his left hand. (similar to having a shield, but yet different.)
That is the 'penalty' he was referring to.
edit: I was 'translating' while Hyper was posting....