Because if you believe in Jesus, you are a Christian, Not a Jew.
You didn't really answer the question.
Why does Israel accept atheists with Jewish parents, but not Messianic Jews with Jewish parents?
A guy I used to work with was a Jew who also believed in Christ. He was very careful to make the distinction between the Jewish religion and the Jewish heritage. Thus he considered himself a "Jew" because of his heritage and a "Christian" because of his belief in Jesus.