I don't think Michael's hatred has ever really been explained besides little hints like Michael considers him a corporate employee, not a member of the "family" and Toby is usually the one who tells him to stop doing something inappropriate.It's funny as someone who just started watching recently I couldn't understand their animosity towards him. It was funny because there was this guy that Michael hated who was like just some guy.
Well to be fair he really hates Toby and he just replaced his girlfriend. I can understand Michael being so angry he wanted to frame Toby (and remember he eventually did the right thing by telling the police the "drugs" were his).I love this show but Michael's behavior towards Toby is too over the top, even for a character like Michael. It's getting so Michael is being such an asshole that you begin to hate him and root for Toby, which I don't think is what the writers want.