Simon will be out for nine months after rupturing his anterior cruciate ligament in his left knee during the 37-16 defeat to Ireland in Dublin last Saturday.
Jon said: "Simon being ruled out is a huge setback for Scotland as he is one of our best players and has been one of the most consistent performers over the last few years. However, as a professional player you have to take your chance when it comes along. I will be looking to push my case forward in the remaining games of the season with Glasgow.
"Everybody involved with the Scotland set-up always knew it was going to be a difficult season after losing so many players after the World Cup. Matt has brought in so many new systems and great ideas. But the Six Nations is not the most forgiving of testing grounds to implement them.
"His first match in charge was in the game against Wales. There was no autumn series in November, as their usually is, for him to ease into things. The players know what the coaching staff are trying to do and we are all right behind them. It is going to take time, but we are all confident it will come.
"The game on Saturday was a big step in the right direction. It was probably our best performance in the Six Nations. But we can't be content with it. We have to keep improving until we are winning again.
Matt Williams has been criticised for agreeing to take his squad Down Under to face the World Cup finalists in two test matches after such a difficult season.
However, Jon disagrees, saying: "There would be no benefits for this team playing against one of the lesser nations after the Six Nations. The young guys who have come into the Scotland squad this season are going to have to learn to test themselves against the best. I am available and will enjoy it if I am selected to go."