Well, you are focusing on the "acid" part of amino acid, rather than the "amino" part. The term amino acid comes from the fact that the backbone is made up of an amino group (normally basic) and a carboxyl group (normally acidic). However, none of that really matters at the end of the day since the vast majority of an amino acids properties derive from their side chains, not their backbone.

Side chains are what make the 20 amino acids different from eachother. Some are basic, some are acidic, some are polar, others nonpolar. While we don't fully understand the process, these properties are what allow a shape to be derived from an amino acid sequence. The particular properties of the side chains control what they are attracted and repelled by, which, in turn, determines how they fold in vivo. So a given protein is made up of basic and acidic bits, all folded up onto one another to produce a new molecule with its own emergent properties, which may, itself, be acidic or basic.