Whatever Gilligan says, I think the character is meant to elicit some sympathetic or empathic reactions from the audience. We wouldn't be interested in him if the character wasn't designed that way.
Early on we have a great deal of sympathy as he is an ill, underpaid teacher facing a bleak future and we don't know how he will provide for his family. We follow his choices. We understand his bad choices as his circumstances make them, at least at the start, credible and don't leave too many alternatives. We wonder how his choices will play out over time: what else will he be prepared to do and how will he respond to the downward spiral he seems to have been forced into.
Sure, he starts to change. He becomes less downtrodden as the Heisenberg element of his character grows and becomes stronger. But somehow we still sympathise because we know where he started. As the level of evil acts grows he might lose some of our sympathy (I mean we don't want to be like him and we know he is doing bad things) but we start to respect him instead. We still care about what happens to him. Besides, he is nothing like the most evil person in the show so we still have relative sympathy for the battles he fights against even more evil people.
To hold our attention for the full run is a great piece of writing as this is much harder with characters doing obviously bad things. But since the universe he is in is filled with even worse people, he is the character we identify with. In fact he becomes a true antihero in the same vein as "The Man With No Name" in the Clint Eastwood movies (a man we root for despite him being a killer for hire: we support him because he does some good despite being a character we would normally classify as a bad guy).
By the end his character may not deserve our sympathy, but he gets it because he is the least bad in a land filled with even worse characters and he does some good things even though he also does many that are evil.