While I like Mac, I also find his sometimes self-righteous, condescending and hypocritcal behaviour to be irritating. It almost feels as if he doesn't fully trust the people he works with to do the right thing unless he first tells them what the right thing is.
Although he gives everyone on his team a hard time on occasion, especially Danny, I would agree that lately his holier than thou attitude has been most pronounced in his dealings with Flack. To me, Flack has never shown Mac anything other than total respect. Although I definitely think Mac respects Flack, he could of shown his respect by handling the situation in 'Consequences' in such a way as to ensure Flack wouldn't get caught in the middle. It never even should have occurred to Mac that Flack wouldn't do the right thing because, as Top41 has already mentioned, Flack has never given Mac any reason to doubt his integrity.
On a related note, I find it interesting that, despite their differences this season, Flack is still watching out for Mac. He intervened with Capt Gerrard to enable Mac to talk to Hawkes in 'Raising Shane' and, more recently, he gave Mac a heads up that he may soon start to feel some heat for questioning a councilmen's son in 'What Schemes May Come.' My hope is that it is Flack's words or actions that enable Mac to get out of the difficulties he's going to face in the final four episodes. Since Mac saved Flack's life last season, it would be nice to see Flack save Mac's career this year.