You have to distinguish between the book Uncle Tom’s Cabin and the character of Uncle Tom.
Uncle Tom was never intended as a positive role model—he was meant to show that acceptance and submission wouldn’t save slaves from terrible abuse. There are other slaves in the book, like Eliza and George, who defy their enslavers and escape—it’s them, if anyone, who embody Stowe’s idea of the rational reaction to enslavement.
That said, Tom was still meant to be a sympathetic character (and an example of Christian forgiveness); but over time, he’s come to be seen more negatively as an enabler. I don’t know if the book’s original audience would have disagreed with that assessment, or cared either way—the point of the book was to criticize the behavior of the slaveholders, not the enslaved.