as annoying as he finds her and as much as they piss each other off, jack is actually so supportive of mariner. he's always rooting for her, (ignoring the whole giant head thing), looking out for her, and he knows that she has such potential.
the times we see him man up and apologise, express and acknowledge his wrongdoings are because of mariner
one of the few times we see him openly doubt his captain is when carol decides to transfer beckett to starbase 80, asking if she knows what shes doing, and telling her to think about it - all for mariner.