Why do amino acids hydrogen bond rather than ionic bond when they are forming secondary structures in proteins? When peptide bonds are formed between amino acids, electron delocalisation causes the N to be more positive and the O to be more negative. As a result, why does 'hydrogen bonding' occur to form secondary structures such as alpha helices and beta pleated sheets, rather than 'ionic bonding'? 

Is this simply a case of semantics, or is it the lack of transfer of an electron that makes the distinction between the two?
(this should be a comment)
I think you are not quite understanding the concept of partial charged or charged. The N atom in the polypeptide chain (so the N in the peptide bond) is partially charged! to be in an ionic state it should have 4 bonds instead of 3. 
 The peptide bond which is formed(above) just contains a N atom which is bounded to three other atoms. The oxygen atom is also partially charged but not charged! read this about H-bonding and partial charge