Kia Joorabchian insists the decision to leave and the Villa job becoming available was purely coincidental.
Joorabchian told talkSPORT: "He feels that the time has come for him to sit aside and see out his ambition. He would like to have a go at the top four.
"At some point in time maybe he'll get a club either in this country or abroad that will give him the opportunity to have a go."
Joorabchian added that reports linking Hughes with another job are just coincidental, and that there has not even been contact between them and Aston Villa.
"All his career as a player and a manager he is a very sincere man and he definitely, definitely does not have anything else lined up," he said. "We've not spoken to anyone.
"I know that there is a lot of speculation about Villa but it is just pure speculation. I have never spoken to anyone at Villa. Villa have never attempted to contact us and we're perfectly comfortable with that situation.
"Mark's sincerity is one of his greatest attributes and if he carried on into this year and signed a contract with Fulham and was looking over his shoulder that a top four club come up then it wouldn't be fair on Fulham."