Maryland was founded as a refuge for Catholics and for a time had a religious tolerance act. However, the colonies were still subject to the English Test Act and Catholics like Carroll (as well as Protestant Nonconformists) could not hold public office. Independence and the First Amendment changed all that.
Just another example of how the First Amendment was not intended to drive religion out of public life, but to allow adherents of all religions to participate in public life and worship how they pleased.