The Constitution and the US Supreme Court have not always recognized that all Americans have civil rights?

No. Many groups, particularly African-Americans and women, have been denied rights guaranteed by the Constitution. The document itself was not written to discriminate against anyone; however, the Supreme Court's interpretation of the Constitution has been used to justify laws and policies withholding civil rights to such an extent that the Constitution had to be amended explicitly to extend protection to (almost) all classes of individuals.