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The pair, Williams and Embleton, have faced the brunt of Swindon supporters' anger on online forums, a radio phone-in and in person on Saturday during the 0-0 draw with AFC Wimbledon, but Thompson leapt to the defence of the club's management staff.
"Against Bolton it was disappointing but I didn't think they did anything to win the game," Thompson said post-Wimbledon.
"We conceded an own goal in the last few minutes but, for me, that (should have been) a point there and it is frustrating and I do think sometimes things do get taken slightly out of proportion.
"It has been 13 games and I appreciate that is a quarter of the season gone but as a whole I don't think the performances have been too bad."
Tempers flared at full-time with a section of the Swindon support taking their issues up with Williams and Embleton directly as frustrations with the poor form boiled over.
"What I saw at the end there, after a battling performance (and) after nine days out - a section of the fans abusing two of the most passionate coaches I have ever worked with.
"Alright, they are not jumping around on the touchline but they work every hour of the day to improve this team.
"They work tirelessly and it pains me to see that (people say) they haven't got passion, that breaks my heart."
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