I think Michael blamed Fredo for a few things, including being a stuff up when it came to the shooting of his father.
Also Michael never wanted part of the family business, but because Fredo was supposed to be next in line, but was too "stupid" to take over as Don, the responsibilty was thrust upon Michael, which I think, he resented him for. Then when he found out that Fredo betrayed him, it just blew everything out of the water.