In Johnson's absence they beat Port Vale 1-0 at Huish Park, but fell 4-1 to Southend on Tuesday - despite taking the lead through Phhil Jevons.
And club chairman John Fry insists that Thompson will continue to enjoy the board's full support.
He said: "Steve Thompson is in charge at the moment and we all feel comfortable about it.
"He's under contract, the players are happy about it and he's happy about it."