I'm sure I've said this before, but it makes perfect sense.
Whether Hogan was a hell or face, or whether Heenan was a heel or face, Heenan always hated Hogan.
He hates the dude in real life, and he's always been against him as an announcer or manager.
It's like one of the longest fueds ever, Heenan never trusted Hogan in any way, so it makes sense that he would question his loyalty here, like he had always done.