With the Scots trailing by three goals by half-time, furious fans called for Burley's dismissal throughout the second half at the Cardiff City Stadium before the players left the pitch to boos at the final whistle.
"It wasn't just the manager, it was all of us who were getting it," Naismith said.
"I can definitely see the fans' point of view. If I was a fan in the crowd, I would have been doing the same. It wasn't good enough. They travel a long way and pay a lot of money hoping to see a good game. We destroyed that basically.
"The manager is the boss and he is the one who is going to get the stick but it's everybody. He's not the one who goes out on the park and wins the games - that's the strikers. And he's not the one who goes out on the park and defends - that's the defenders.
"Basically, everybody who played has to have a hard look at themselves. The only positive was that it was a friendly and it's not cost us in a European or World Cup game."
Scotland were left reeling when goals from David Edwards, Simon Church and Aaron Ramsey handed the home nation an overwhelming advantage in the opening 35 minutes.
And, despite all six available substitutes being thrown into the action after the interval, the visitors simply had no reply.
"We lost three goals in pretty quick succession and that has basically lost us the game," said Naismith.
"It's the whole team. I think I was partly at fault for the first goal for not tracking my runner.
"All three goals could have been avoided and that was the problem. We had a couple of chances early on but after we lost the three goals it was all over."
Scotland have suffered defeat to both Japan and Wales - and shipped five goals - since their failure to secure a play-off spot for the World Cup finals in South Africa next summer.
Burley's record as national team boss now stands at just three wins in 14 attempts but Naismith is confident Scotland do have the quality needed to transform their fortunes ahead of their next campaign.
"Definitely," he said. "We showed in the last two games of the World Cup campaign that we have.
"We played against one of the top four teams in the world, Holland, and for 60 minutes we gave as good as we got and we could have been a goal or two goal up.
"We also played Macedonia, who have shown they can be tricky opponents, and we showed we could beat them.
"So we've definitely got the squad. I can't put my finger on what went wrong with this game but I'm sure it's something the manager will be looking at over the next couple of months."