I used to think this referred to the atheists who challenge your faith. But now it means a lot more. Recently, after a great deal of soul searching, I left a church I had been very active in for many years. I prayed and this was what I got - to leave and focus my efforts elsewhere. The congregation was shocked for the most part, and perhaps even angry. Many thought I had been led astray. It never occurred to them that I had prayed earnestly, and this was His guidance. Rather there was a chorus: "Where is thy God?" I am afraid I might have been a part of that chorus at one time. Humbling!!
This beautiful Psalm 42 speaks to this kind of situation - every earnest seeker for truth will experience it. The First Edition of Science and Health speaks plainly about it:
"Christianity is not dishonest, but our religions are; to rule mankind and conciliate society at the expense of Truth, yea, to be popular is the weakness of the world. He that leaves all for Truth, and is falsely accused and hated because of Christianity, is wise; the world will believe error and be slow to admit Truth."