Why is Tod Clifton shot down? I am aware of one reason (his being black) but I feel like there's more to it than that.
You're right. There IS more than that. However, the secret to Tod Clifton's character runs deeper than the reason for his death. Tod Clifton is the martyr of The Invisible Man, a semi-Christ figure crucified for his affection for civil rights.
We first see Tod Clifton when our narrator meets him and, slowly, he becomes a very important character. Very active in the group called "the Brotherhood," Tod and the narrator bond over a fight in the street with "Ras the Exhorter" who is a black nationalist. Ras is abrasive and argumentative, chiding Tod for working with white men at all. It is Tod and Ras who convince the narrator to become active in the Brotherhood. Tod, of course, is the leader of the black youth in Harlem. Tod is captivated by Ras due to Ras' very Caribbean take on being African. Tod's goal is to fight for jobs for the black youth.
It's you young folks what's going to make the changes, y'all's the ones. You got to lead and you got to fight and move us all on up a little higher. And I tell you something else, it's the ones from the South that's got to do it, them what knows the fire and ain't forgot how it burns. Up here too many forgits. They finds a place for themselves and forgits the ones on the bottom. Oh, heap of them talks about doing things, but they done really forgot. No, it's you young ones what has to remember and take the lead.
Eventually, our unnamed narrator is blamed for Tod's disappearance in the brotherhood. What Tod is doing is very ironic, actually. Tod Clifton, always an advocate for jobs for black youth, is selling Black Sambo dolls on the street. The irony here is that "The Story of Little Black Sambo" has become an iconic story leading to racism toward black people. It is about a little black boy who is forced to give up his clothes, piece by piece, to save him from tigers. Because the tigers are vain, they fight about who is the most beautiful and chase each other around a tree until they become a pool of butter. Sambo then gets his clothes back. The story has become so iconic that the word "sambo" has become a racial slur. Tod, a member of the proud Brotherhood, should NOT be selling these dolls to white people on the street. It is desperate and the exact opposite of pride in African heritage.
It is while Tod Clifton is selling these Sambo dolls that he becomes a target of the white police and is shot by one of them. When you say "I feel like there's more to that," what you are talking about is that Tod is more than just a black man peddling items. Tod is a public figure for the Brotherhood: an icon and a martyr for the cause. THIS is why a riot immediately follows. The riot is less about Tod's death than a reaction to the murder of the Brotherhood's icon.
In conclusion, it's important to realize why Ellison named the character "Tod." In German, the word Tod means "death" or "dead." This foreshadows Tod's fate at the hands of the white police.