God Bless America was trotted out on a radio broadcast during an Armistice Day celebration in 1938, it was intended to be sort of a peace song because Hitler was beginning his rise to power in Germany.

This Land is Your Land was Guthrie's response to that song, he thought it was too idealistic. The song was originally called God Blessed America For Me (sort of sarcastically). One of the original lyrics that is not sung in the song now: "One bright sunny morning in the shadow of the steeple, by the relief office I saw my people. As they stood hungry, I stood there wondering if God Blessed America for me."

Her performance was not an overt protest, no. But I don't think her choice of those two particular songs was simply because they're nice patriotic songs. I have no doubt she is aware of their history (I was and that's just because of a random music class I took in college) and that they were chosen for a specific reason. Knowing her political stance, I can only guess what that might have been.