You are quoting verses that specifically say that they have, in large part, been cut off. You even ignore the first part of that chapter:
"But what saith the answer of God unto him? I have reserved to myself seven thousand men, who have not bowed the knee to the image of Baal. Even so then at this present time also there is a remnant according to the election of grace. And if by grace, then is it no more of works: otherwise grace is no more grace. But if it be of works, then is it no more grace: otherwise work is no more work." (Rom 11:4-6)
So here Paul gives a historical example where the largest part of the Jews were damned and cut off from grace, save for a small remnant who are saved, not according to their innate "holiness", but according to God's mercy.
And it is only those Jews-- or Gentiles-- who are the children of Abraham inwardly, that are the true children of Abraham and of God.
who are holy because the root is holy
The natural branches that are cut off are not holy; they are condemned, and will be burned.
The branches are holy because the root is holy, and even those broken off may be graffed into their own olive tree again. Do not boast against the branches.