Harriet Beecher Stowe was white. She came from a 'well to do', very religious family and her representation of Uncle Tom caused many reactions. The uproar from black people (both then and now) mainly came from the fact that was presented as being quite docile and submissive (even though this is presented in a Christ like way). He also comes accross as having a feminine side, which again, wasn't received well. The problem was that Stowe was a sentimentalist, and she tried to combine the essence of sentimetalism - feeling - with slavery and thereby change peoples' attitudes - in simple terms, appeal to hearts rather than minds. Arguably this worked for some, but for others, such as white male slave owners, it was too difficult to make the jump from seeing slavery purely in practical terms to emotional terms. However, it's important to make the distinction between then and now - in my dissertation I contrasted attitudes both at the time the text was written and the present time. There was also controversy about the way other black people were presented - I can't remember exactly, but I'm sure there is a part about some black children which by today's standards appears racist.
There was the problem of Eva and Topsy - Topsy is portrayed (I think) in racist terms by today's standards. She's wild, unruly, ugly, compared to Eva, who, as her name suggests in angelic. Tom's 'friendship' with her was also problematic. Readers found it too difficult to believe that an angel would love a black man, and in one part it is suggested that black and white would become equal in heaven which was just too much in those times.
With regards to To Kill A Mockingbird - I didn't read this until last summer, purely for leisure, and although I thought it was fantastic, I haven't studied it with an 'academic' mind! From what I can remember, Lee presents the black man accused of rape in a very positive light (? correct me if I'm wrong). I think it's also written in a very different style and obviously a few decades on. God, I could really get my teeth into this - I wish I were doing my disseration again!