Massa Waller's a nicer guy than his brother (Kunta's first owner) but that doesn't mean much in the grand scheme of things. It's like saying that a hammerhead shark is less dangerous than a great white.
It's true—but if you cross paths with either of them, you're going to end up with your head bitten off.
Being a doctor by trade, Massa Waller has the natural disposition of a caretaker. In fact, he purchases Kunta in the first place because he's opposed to his inhumane abuse Kunta receives at the hands of slave catchers. He even tends his wounds. In a similar way, Massa Waller provides his slaves with far better living conditions than other plantations.
Despite this, it's clear that Massa Waller perceives black people as less than human. Think about all of the conversations he has in front of Kunta as if he wasn't there. That obliviousness is symbolic enough, but the content of those conversations is typically horrifying.
Here's a representative sample:
"You don't know who's shuffling and grinning and planning to cut your throat. Even the ones right in your house. You simply can't trust any of them. It's in their very nature." (58.18)
Basically, Massa Waller treats his slaves just well enough to ease his guilty conscience, but not well enough to respect their humanity. It's because of men like Massa Waller—men who refused to own up to the evil they perpetrating—that the American institution slavery become such an integral part of the fabric of the country.