The Stoke City boss says the forward is "desperately disappointed" after having been given his marching orders and feels the suspension will hit his side hard
Walters had equalised Bradley Johnson's header from the penalty spot on 73 minutes, but was given his marching orders shortly afterwards for a knee-high challenge on Alexander Tettey.
As a result, Walters will miss crucial upcoming games against West Ham, Aston Villa and Hull City - who are all in the fight for survival along with Hughes' side.
Hughes is already without Charlie Adam due to a suspension, though he hinted that the club would not appeal Walters' punishment.
"There is contact," the Welshman told reporters. "Jon's accepted he did catch him but the ball's bouncing between two players, both players have got their feet high unfortunately he did catch him but I did think on this occasion the punishment's a bit harsh for the crime.
"We're looking at Jon missing three games for that and it's deemed serious foul play and I just think it was one of those that are a matter of millimetres whether or not contact is made.
"It's unfortunate for Jon. I don't think he's been sent off at senior level so he's desperately disappointed he's had to depart in those circumstances."
The suspensions of Walters and Adam have added to knee injuries for Oussama Assaidi and Robert Huth to stretch the resources available to Hughes ahead of next week's home clash with West Ham.
"It's difficult for us at the moment," he added.
"We're a little bit short on numbers, we've just got to make sure next week we get everybody fit and well and make sure we're ready to go with enough numbers for a big game next week."