Was Bush speaking solely about right-wing extremism? There is no evidence that he was. The reference to January 6 seems pretty clear in the reference to “defiling national symbols,” though you could also read it as referring to left-wing protesters who topple monuments.
Personally, I think that Bush’s comparison between domestic extremists and the September 11 terrorists was a bit of a stretch: at least so far, no American domestic terrorists other than Timothy McVeigh have shown a level of disregard for human life comparable to al-Qaeda (or ISIS). But “not as bad as Al Qaeda” is a pretty low bar, and as McVeigh’s example shows domestic extremism certainly has the potential to lead to carnage.
I do think that Bush’s criticism was more for the right than the left; he singled out nativism and anti-Muslim bigotry but not left-wing ideological shibboleths such as the tendency to see “white privilege” everywhere. But the way things work in a moment of cultural and political polarization is that the only effective way to counter bad ideas is for people to attack bad ideas in their own camp.