The short answer to this is that the Maryland Act of Toleration gave religious freedom to all Christians but not to anyone else.
This law was meant to protect the religious freedom of various Christian sects. Maryland was settled by Catholics wanting to escape religious animosity in England. They realized they would need Protestant settlers as well in order to have a viable colony. This was a major reason for the creation of the Act of Toleration.
In this act, all Christians were given religious freedom. The act said that no one
... professing to beleive in Jesus Christ, shall from henceforth bee any waies troubled, Molested or discountenanced for or in respect of his or her religion...
This protected the right of all Christians to believe and to worship as they wished.
However, those who were not Christian were not protected. In fact, they were at least officially subject to the death penalty. The act said that anyone who would
... deny our Saviour Jesus Christ to bee the sonne of God, or shall deny the holy Trinity the father sonne and holy Ghost...
would be subject to penalties such as
... death and confiscation or forfeiture of all his or her lands and goods...
From this, it is clear that religious toleration was extended only to Christians.