It has nothing to do with Ailes. MM went to the advertisers and threaten boycotts, negative on-line campaigns. etc. and the advertisers caved.
Yes, That started way back in 2009 but Beck still got sponsors they couldnt intimidate, Goldline was an example. My guess is that Ailes thought Beck didnt fit in with the rest of the network (as well as the sponsor problem) , and beck certainly defied the convention. Compare Beck with RINO/Hannity.
There were some of his shows I absolutely loved, but others bored me to death. He would pick single theme and do it for days and days. When he played vids of Democrats and used humor he was at his best.