Samuel Morse, along with other Know-Nothings, believed that Roman Catholics could not be good citizens of a republic because of the hierarchical nature of their religion.
The Catholic Church is hierarchical. Priests are said to know more about what God wants than lay people. Priests have to obey bishops who have to obey those above them. All are supposed to obey the pope.
To Morse, this meant that Catholics were naturally inclined to allow themselves to be tyrannized. He says that they had been educated to simply obey those above them and that they would do so rather than thinking for themselves. Morse claims that they were “but senseless machines” who “obey orders mechanically.” This is not, Morse says, appropriate for citizens of a republic.