There's a nice line in Part II when Mike asks Tom about what Fredo knows...'He says he doesn't know anything, and I believe him'
I like that line, whether its true or not, who knows, but Tom seems to be trying to protect Fredo.
You're right to cite that scene because it does show that Tom was trying to protect Fredo...
I don't know that this was necessarily to 'protect' Fredo than to simply concur that the guy really doesn't know anything. It may be true that even Michael believed that Fredo was 'kept in the dark' as he said he was.
The significance in Tom's feelings toward Fredo after the betrayal is not necessarily what Fredo 'knew', but in what in his greed and stupidity Fredo had caused to happen.
Apple