Although Northerners became progressively more outraged about the institution of slavery as the nation approached a civil war, it would be inaccurate to say that Southerners were prejudiced against blacks and Northerners were not. Slavery was actually present in most of the American colonies, but the rapid growth of industrialization in the North and the thin, rocky soil of New England had led to slavery's slow but steady death because of its lack of profitability north of the Mason-Dixon line--not because Northerners had a sudden surge of conscience.
That being said, the North was a safer place for African-Americans for obvious reasons, and there were people who were happy to help provide safehouses for Harriet Tubman's "Underground Railroad", particularly when first one, then another Fugitive Slave Act was passed by Congress in unsuccessful attempts at compromise with the South. Activists like William Lloyd Garrison were very good at galvanizing support for their causes, and although Northerners weren't necessarily the liberal humanitarians the books sometimes portray them as, abolitionist sentiment grew rapidly in the years before the war.
For its part, the South, particularly wealthy planters, worked hard justifying their feelings about blacks, and the slavery system. For many years, Southerners quoted the Bible as they explained to slaves why they (slaves) should be satisfied with their lot in life; after all, it was clearly God's will, Southerners said. Southerners also like to compare slavery to the horrific conditions in many Northern factories, saying that their slaves were fed and clothed and sheltered while factory workers simply worked inhumane hours under awful conditions for little pay.
After slavery and the Civil War ended, African-Americans faced new challenges; in both North and South, many people resented competing with newly freed slaves for jobs. The South, of course, actively created legislation over the years to keep blacks from enjoying any rights at all, while in the North, it was at least possible to live safely, if not completely free of prejudice.
The paradigm I find most helpful in being able to dissect the bias against African- Americans in the South and in the North is the covert vs. overt racial understanding. In his autobiography, Malcolm X explores this dynamic and I find it very helpful in understanding the nature and dimensions of racism. I would suggest that there was an overt demonstration of racism in the Southern part of the United States. This was expressed in the root base of slavery, where biases against African- Americans were so intensely evident. After the Civil War, overt racism bias was seen in the Jim Crow legislation that sought to deny rights to newly freed people of color. At the same time, this was also evident in voter intimidation attempts as well as physical harassment. Lynchings were also intrinsic to this overt racism. While not as demonstrative in the North, covert racism bias was shown in different forms. This was in the not so subtle "designation" of parts of living areas where it was unofficial code that people of color could not live there. At the same time, the bias of covert racism was present in how social services were denied to the parts of towns where people of color lived. Garbage was not picked up as regularly, police did not walk the beat as often, and parks in which children could play were more dilapidated. Covert racism denied fair housing practices to people of color as well as sought to limit economic opportunity. In both demonstrations of bias, there was a thorough expression of the difficulty in being African- American in America.