The England international has been in the media spotlight for days after lurid allegations about his private life surfaced last weekend.
On Friday night, Rooney and his wife Coleen issued a statement asking for privacy at a difficult time.
Ferguson said he left Rooney at home rather than allow him to run a potential gauntlet of abuse from fans who used to adore the striker when he wore a blue shirt.
However, Phelan suggested that there were other considerations in the decision not to take the 24-year-old back to Merseyside on Saturday.
"Wayne wasn't ready to play so we didn't play him," he told BBC Radio 5 Live.
Phelan's comments add weight to the widely-held suspicion that there was more to the decision than Ferguson was letting on when he spoke in a television interview just prior to kick-off at Goodison.
"We made a decision simply because he gets terrible abuse here. We don't want to subject him to that," Ferguson told Sky Sports.
Leaving out Rooney for such a reason was most unlike Ferguson, who usually has absolute faith in his players to cope with what is thrown at them - sometimes literally - as United players.
In the past though he has not been afraid to leave out his big names for a variety of reasons, famously dropping David Beckham after growing tired of his off-field lifestyle, and having to deal with the outspoken criticism from within of former captain Roy Keane.
The United boss did confirm after the 3-3 draw, when his side conceded two goals in injury time to squander three points, that Rooney would be back in the starting line-up for Tuesday's opening Champions League encounter against Rangers.
When asked whether the players missing on Saturday would be back on Tuesday, he said: "They will all be available."
Rooney was fully expected to play against Everton but despite being at the team hotel in Salford on Friday night, he did not even get on the team coach to make the relatively short journey along the M62.
Despite Everton fans directing plenty of vitriol at their former hero on his early returns to his former stomping ground, the reaction has mellowed on the last couple of visits.
But considering the week Rooney has had, Ferguson felt it was better for him not to be on Merseyside.
He refused to comment on the situation further after the game, having said 24 hours earlier he would not discuss matters which did not directly involve the team.
"Let's put it to bed straight away. I am not discussing any of my players' personal lives," he said at his pre-match press conference.
In their statement on Friday night, the Rooneys admitted there were "issues to resolve".
"The last six days have been extremely painful for us and for our families," the couple said.
They added it was impossible for them "to attempt to resolve any issues in the current media glare".