The Australian believes there is a long road ahead before Scotland can be a major force in world rugby.
"The Scottish public will be disappointed with the outcome of the fixture, but this gives us a clear indication of where we are," said Williams.
"There is still a lot of work to do. I could not fault the attitude and work ethic of the guys, but there are aspects of our game we can't be happy with.
"But there are no short-term solutions to the problems of the national team. There are only long-term solutions, and I have said that all along.
"I was happy with our line-outs and scrums, but the area where we are disappointed is in our defensive phases.
"We need to learn from that and the fact that we did not implement the systems that we wanted to."
Williams also admitted Scotland will have to wait before discovering how serious the injury to centre Brendan Laney is.
Laney went off after his hand was stamped on. "It's very swollen," added Williams "It could be a break - but we will just have to see."