How are amino acids neutral at physiological pH?
You are right, most of the amino acids have pI around 6, so they are slightly negative at pH 7.


Calculating approximate isoelectric points for amino acids and peptides


The isoelectric point depends on the amino and carboxylic-acid groups and the groups of the side chain. E.g. lysine has an amino group on the side chain, so it has a pI of 9.74.