Rutherford addresses the issues of the lawful authority of the Civil Magistrate, and the proper relationship of Church and State. He is the first to make a theological argument for the lawfulness of resistance in the matter of the king's unjust invasion of life and religion. Here are some excerpts from Lex Rex…
Arg. 1: That power which is obliged to command and rule justly and religiously for the good of the subjects, and is only set over the people on these conditions, and not absolutely, cannot tie the people to subjection without resistance, when the power is abused to the destruction of laws, religion, and the subjects. But all power of the law is thus obliged, and may be abused by kings, to the destruction of laws, religion, and subjects.
The proposition is clear. 1. For the powers that tie us to subjection only are of God. 2. Because to resist them, is to resist the ordinance of God. 3. Because they are not a terror to good works, but to evil. 4. Because they are God's ministers for our good, but abused powers are not of God, but of men, or not ordinances of God; they are a terror to good works, not to evil; they are not God's ministers for our good.
http://www.apuritansmind.com/SamuelRutherford/SamuelRutherf ordLexRex.htm