Stanton was jeered by Essendon supporters when he was subbed out of the Bombers' game against West Coast at half-time on Sunday due to a shoulder injury, but Thompson said the 25-year-old had the support of the club.
"Up in the box you don't hear crowd noise, but we found out after the game. It's amazing our supporters can do that," Thompson said.
"I thought most of the things we've done this year have been pretty positive. From the coaches' perspective, from Hirdy down, we all love what Brent Stanton does for the team.
"He's a leader of the team, he takes people with him, he trains exceptionally well. We rate him as one of our best players, so to think our supporters would cheer him [being subbed off] amazes me.
"The club is behind him 100 per cent and we'd like our supporters to get behind him."
Meanwhile, Thompson said Stanton, and veteran defender Dustin Fletcher, still had to prove their fitness before facing the Brisbane Lions at the Gabba on Saturday night, a game which the two-time premiership coach said was important given the club's poor record interstate.
"Stanton is probably our biggest concern. [Dustin] is one who is a bit of a concern, but he's probably ticked more boxes than Brent at the moment," he said.
"We just have to give the guys a belief that if they do what they've been doing then we'll go up to Brisbane and be competitive.
"It doesn't really matter where you play, you just have to put in the same effort every week. Good teams can win interstate."
Callum Twomey covers Essendon news for afl.com.au. Follow him on Twitter at @Cal_Twomey
