As long as the prejudice is bound in the context of the story, then I view it as being totally acceptable. The character's views don't have to be those of the author, and the author could even choose to deconstruct those views in the way they are presented in the story, with the prejudice perhaps coming from a gap in the character's knowledge or some irrational hatred that is exposed as such. More than likely, this prejudice will be in line with commonly held views of the time period/location.
In the end, the author isn't telling their own story, or conveying their own thoughts. The character is a separate entity, and we shouldn't worry about what they think, more why they think it and how it affects their characterisation. I also think its entirely possible to have a likeable character who is prejudiced or even racist, considering there are figures of history that many consider to be 'likeable' that held questionable views and prejudices.