Steve Ray has a list of 35 loaded Questions for "Bible Christians" (quotation marks his)(link to the whole list). This is number 35/35. I'm trying to provide the answers in a common format, for easy reference.
35) Hebrews 13:17 says, "Obey your leaders and submit to their authority. They keep watch over you as men who must give an account. Obey them so that their work will be a joy, not a burden, for that would be of no advantage to you." What is the expiration date of this verse? When did it become okay not only to disobey the Church's leaders, but to rebel against them and set up rival churches?
1) The second coming of Christ is the expiration date on this verse.
2) When there is a conflict between what religious leaders command and what God commands:
Acts 5:29 Then Peter and the other apostles answered and said, We ought to obey God rather than men.
1) Leaving a church is something that should not be undertaken lightly.
2) Although Rome's anti-christian attempts to usurp authority over Christ's church are extreme, there is real authority given to the elders of Christ's church, and they ought to be given qualified obedience.
3) Note that the command to obey our religious leaders is not the only such command in Scripture. We are also commanded to obey our parents:
Ephesians 6:1 Children, obey your parents in the Lord: for this is right.
Colossians 3:20 Children, obey your parents in all things: for this is well pleasing unto the Lord.
And the king:
1 Peter 2:17 Honour all men. Love the brotherhood. Fear God. Honour the king.
Romans 13:4 For he is the minister of God to thee for good. But if thou do that which is evil, be afraid; for he beareth not the sword in vain: for he is the minister of God, a revenger to execute wrath upon him that doeth evil.
But even the most zealous advocates for Romanism recognize that the obedience in these categories is to be a qualified obedience. The same goes for obedience to religious leaders as demonstrated by Peter's (and the other apostles') response to the Sanhedrin.