The Hungarian’s contract with the Cottagers is set to expire this summer.
Gera was sent-off against Arsenal on Sunday for a lunge on Thomas Vermaelen.
“We were desperately disappointed for Zoltan,” Hughes told Sky Sports.
“I’m still hopeful that he’s going to stay next year but he’s got options and he’s keeping them open and he’s within his rights to do that.”
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Since Guus Hiddink arrived at the helm, Chelsea have improved considerably after a tricky start to the campaign.
Newcastle United are staring down the barrel of relegation to the Championship for the second time in the past eight years.