The hosts were always in control after former Glovers striker Andy Williams had given them a 24th-minute lead, with James Hayter's header proving mere consolation.
Johnson said: "We were outplayed, outfought and they were cleverer than us. The score was a fair reflection. Swindon were better than us individually and a few of my players did not turn up.
"A few home truths were said after the game and we will be training on Sunday morning to sort out a few things that need sorting out.
"We do not have the quality they had in front of goal. They are also more experienced than us and our youngsters have a lot to learn.
"Some of our players go missing when we go to the bigger places but we cannot change anything until January. We will get there in the end."