The 25-year-old has failed to make an impression since his arrival in the summer and was subject to boos from the home fans when he was introduced during Saturday's defeat to Stevenage.
Walton responded by cocking his ear in the direction of the Town End and was subsequently jeered following his first few touches.
"I don't know if the supporters were booing him or my substitution?" Hughes told the Hartlepool Mail. "Let's say it was the latter. If not, try to cheer him and let me boo him if needs be!
"I thought he came on and slotted in the midfield role deep and never gave the ball away. He has a part to play and has worked very hard in the weeks he's had off with injury and he is a really good footballer."
The former Leeds and Charlton man recently returned from a hamstring problem and Hughes has challenged him to compete with Paul Murray for the anchor role in the middle.
"Simon's got a big part to play," he continued. "I'm going to have to sit him down and tell him that. Murray is an absolute trooper but it would be nice to have another option."