In short, because they were easy targets. That is, much like the Jews in Europe and later in the United States, it was easy for society to discriminate against African-Americans, especially since it benefited whites economically. Skin tone just made it simpler yet, much as it did with Asian-Americans in the 19th and 20th centuries. Once a generation had passed since Irish or Italian immigration, for example, it was almost impossible to tell the difference between them and other white Americans, so there was less discrimination over time. I also think it's important to remember, or at least consider, the idea that racism in this country likely started because of slavery, not vice versa.
This is a good question. I don't think it has as much to do with skin tone as it does some other things; but, of course, the skin tone made them easy to identify. First of all, the slaves were a powerless class; no one spoke for them. They were relatively cheap labor, at least in the beginning. They were "used" to the heat, so they could do the work that was required in the South. And they gave everyone someone else that they could feel superior to, that they could treat with contempt, no matter how miserable the condition of the one doing the treating.
The blacks were not the only ones who received this kind of treatment; it was the way many minorities were treated in this country. Take the Irish, for example. In his video treatment, "New York," Ken Burns points out that, in the process of building Central Park in New York City, the Irish were hired only AFTER all the blacks had been hired and were generally treated as a subhuman species. Due to a lot of factors (familiarity with the language, their skin color that blended in, and political power through Tammany Hall) the Irish were able to transition quickly, but it's worth noting that their initial experience, and that of many immigrant groups, was in some little way comparable to that of the Blacks.
The way the powerful treat the powerless is often shameless; it's also part of the way it's always been.