Barry was at the centre of controversy when he inexplicably failed to spot a bad challenge by Thomas Gravesen on Olivier Bernard, in the build up to Everton's winning goal.
But Shepherd has decided that a protest will be of no benefit to us.
"It was all a bit of a nightmare for us and obviously we are not very happy at what happened," he said.
"We don't think the referee did himself justice and he certainly cannot be accused of favouring Newcastle United.
"But we are not whingers and we have never been whingers. It's all in the past now and we will soldier on in the true Newcastle United tradition."
Last season Arsenal complained about the performance of Graham Poll during our 3-1 win at Highbury and as a result Poll did not officiate in a Gunners game for another 12 months.
A year without Barry, Andy D’Urso or Uriah Rennie would be nice – perhaps it is time they followed the Mackems into the Nationwide.