In answering this question, remember that Hobbes's main idea is that the sovereign needs to have complete power over his subjects. This will tell you something about Hobbes's attitude towards religion in government. Hobbes did not believe that any church should have power in the government. The reason for this is that the church's power might interfere with or reduce that of the sovereign. Therefore, no organized churches should be able to wield power.
This is not to say that Hobbes believed that separation of church and state was necessary. Since Hobbes believed that the monarch should have complete power, he also believed that the monarch should have power over religion in the country. The monarch should be able to dictate what religious actions (as opposed to beliefs, which cannot be commanded) were taken or not taken.
So, Hobbes felt that churches should not interefere with the power of the sovereign, but had no problem with the sovereign controlling religion in his kingdom.