AT fields are a metaphor for the emotional barriers we put up between ourselves and others. Barriers that help us feel safe but also prevent us from achieving true intimacy. This ties in to Shinji's arc. There is even an episode of the original series titled "Hedgehogs Dilemma" which is what some philosopher called this dilemma. What the AT fields actually "are" is never really explained but it's also irrelevant to what the show is trying to do and say.