Non-Believers

Not everyone believes Tora to be a goddess. The list is small, but it's there.
Dexter Bright created the Imperial Cult in order to allow Tora to become ruler of the Empire, and therefore doesn't actually buy into it. He also told this to Samuel, his son.
The people of Mt. Calvary, including the Silver Knights, believe Tora to be an avatar of the Light, but nothing beyond this. This is the only reason their religion is tolerated by the Imperial Cult.
Lady Cassandra was told by the Ancestors that Tora was no goddess, but still refers to her as such both to avoid prosecution and out of respect for Tora.
Calorus has great respect for Tora, but was raised with her and knows her not to be divine. Due to his respect for her, however, playing her off as a goddess isn't much of a stretch.
Tora knows she is no goddess, but allows her subjects to worship her out of courtesy to them.