Although Gatsby has flaws, he is the protagonist/flawed hero of the story. One could make the argument that Nick is also a protagonist, but Nick has a more direct function which is to tell Gatsby's story.
There are many issues which contribute to the conflict between protagonist and antagonist in this novel. But the main conflict has to do with the imbalance of opportunities among the rich and poor classes. Gatsby represents the rags to riches story of the American Dream. Tom Buchanan represents a member of the social elite, a member of an owning class who tries to keep those opportunities amongst his friends and family (and his race) and their subsequent generations.
So, Tom is a racist, misogynist brute. In Chapter 1, Nick notes that Tom and Daisy belong to a class of people who have and flaunt these opportunities.
I waited, and sure enough, in a moment she looked at me with an absolute smirk on her lovely face, as if she had asserted her membership in a rather distinguished secret society to which she and Tom belonged.
Consider the fact that Tom mistreats Daisy and Myrtle (and George), in addition to being an elitist, racist only interested in money, prestige, and self indulgence. Then consider that Tom is indirectly responsible for Gatsby's death, assuming that Gatsby himself was driving the "death car" when in fact it was Daisy.