The Iron were comfortably outclassed by MK Dons at Glanford Park, with the loudest discontent from home fans yet who have been treated to a deteriorating standard of football and results as the campaign has progressed.
"I can understand their frustration because they want to see their team winning and we are not doing that," said Knill.
"Things are pretty low at the moment. What will be will be, but I hope to be here next week. No one wants us to be in the position we are in.
"I am disappointed with the way things are going for us at the moment, we are being punished for every mistake that we are making.
"But I still have faith in the players, and they still trust me to help them with their careers."
Karl Robinson, the Dons manager, backed Knill to turn the Iron's fortunes around.
"I know Alan Knill and his assistant Chris Brass very well. They are good men and will turn things around," he said.
"When our own fans joined in with the chants against Knill, I put my hands up to stop them - and they did, which is great credit to them."
The three-point haul ended a three-game winless streak for the visitors, who have finished in the play-off places in their last two seasons under Robinson.
"Scunthorpe is always a difficult place to come and we have the bruises to show how much they wanted to win this one," he added.
"I know Scunthorpe are going through a difficult spell, but We came here with the utmost respect for them.
It was a very professional performance from us.
"You just look at the two goalscorers, Luke Chadwick and Alan Smith, they have both played at the highest level.
"Alan has played for England, Manchester Unitred and Leeds. yet he is still prepared to come here to Scunthorpe on a bitterly cold afternoon and perform."