Machines can be individuals and have different opinions. Some are the enemies of humanity and some are our friends. The benevolent machines are not the prevailing majority however.

Evidence

1. "Some believed that we lacked the programming language to describe your perfect world." Differing beliefs here implies the ability to have differing views elsewhere, such as their perspective of humanity.

2. The Oracle. Several evidences that she- clearly an ally of the Resistence- is a machine.

3. As of this writing, it's become something of an obvious point. Those up on their Reloaded info have read the spoilers regarding allied machines as well as more aggressive ones. The Animatrix clears it up further. But the above two points serve to reinforce the prediction that arose before such materials.