The 31-year-old released a statement last month in the wake of interest from China to confirm he wants to stay at United but that hasn't stopped rumours linking him with a move away in the summer.
The United captain isn't seen as a vital member of Jose Mourinho's plans and was left out of the squad who travelled to Russia.
Jose Mourinho omitted Wayne Rooney from the Europa League squad tonight
Wayne Rooney faces an uncertain future at Manchester United
And former Arsenal midfielder Nicholas can't see a way back for Rooney if players such as Jesse Lingard are being picked ahead of him.
"I think it says a lot that Wayne Rooney has been left out of the squad entirely after a performance that he would have been disappointed with on Saturday," Nicholas told Sky Sports.
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Rooney has started just nine Premier League matches this season
"Yes he was really poor and I think it shows you that his time is coming to an end when he's behind Jesse Lingard in the pecking order.
"Michael Carrick might get a rest but I expect United will go to Russia and set things up to ease through in the second leg."