The reason for this misconception is based on a misunderstanding of the nature of belief. The truth is: belief is not a choice. Belief is a direct reflection of something we hold true. You cannot believe something while simultaneously thinking it to be untrue. To put it in our terms, one cannot believe in God without also thinking that he actually exists. Therefore, what you think to be true you will believe in, and vice versa. This point is obvious, yet overlooked. If one doubts the truth of this notion, one should attempt not believing something he knows to be true, or believing something he knows is not.
The first time I was informed that belief is not choice I was still a believer in God and almost immediately rejected the idea. It was only after stammering out a pathetic response to this claim, that I began to comprehend its validity. As a believer it was very humbling to suddenly realize that what I had once held as a virtue of mine was merely a reaction to an idea I had already accepted.
People generally wish to be considered virtuous to themselves and more so to their friends. It is for this reason that we are so easily convinced that belief in God is a virtue. Belief in God for believers is not a difficult thing to retain. A believer can then be virtuous by the mere act of being himself! Even in the face of the worst suffering, so long as the believer still thinks that the notion of God is true, the most he will feel is anger or hatred toward God. Though the believer may overcome his anger and confuse this with choosing belief over disbelief -- and thereby feel virtuous -- he has done nothing more than fall back in love with an idea he never doubted.
I suspect that the origin of this misconception, promulgated by almost every religion, is far more sinister than simply wishing to be virtuous. When someone thinks that he chooses to believe in God, he then thinks of himself as better than he who doubts God. For as he chooses, so does the skeptic. The believer will then at best, pity the non-believer as we see in the more benign christian sects, and at worst, hate the nonbeliever, as we see in the fundamentalist Islamic regimes of today. Religion therefore sets itself apart from the secular as they who choose to believe in God against those who choose to disbelieve in him.
Once we can admit that belief in God is nothing more than a reflection of what we consider a fact about reality, we can understand the great fallacy in blaming someone for doubting God, or praising one who doesn't. Of course, since our beliefs represent what we consider to be an actual state of reality, it behooves us then to have some evidence for this claim. Is this not the rule regarding everything else? This is why all religious people whom I have met have called on some personal experience, or reasonable argument, or piece of evidence that resonated with them as the reason they believe. I suspect it would be very hard to find a true believer in any religion who does so without some reason or another, at least not admittedly so.
When the reason for belief is challenged in the mind of the believer -- when he actually doubts the principles of his faith -- he will be compelled to find an answer of sorts to quiet his doubts. If he cannot find one, he may begin to doubt other points of his faith, and may eventually leave his faith entirely. What brilliance of certain religions then, to make belief a virtue and doubt a sin!
The "virtue" religion is actually referring to is that of allowing oneself to be credulous to the supernatural, obedient to the religious authority, and to not question the "truths" it espouses. They seek not to excite your investigative mind, but rather to inspire your feeble heart. Why else would religion praise blind faith over honest skepticism, if not to keep the wolves far away from the sheep?
Doubt too is not a choice. One can only choose to question the assumptions he has been taught. One can look for truth at the risk of his convictions. One can choose to be unafraid of what one might find... does this not seem virtuous?
It is the skeptic who stands in opposition to religious dogmas, or societal convictions. He casts aside any unproven claims about reality and ventures forth to see them for himself. He does not wish to be told that faith requires him to not know, for to him that sounds suspicious and rather stupid. He does not need some clergymen to lead him shackled and comfortable; he is brave enough to face reality on his own... as a free man.
Doubt has another feature that sets it as more positive than belief. It was best said by the English actor Sir Peter Ustinov: "Beliefs are what divide people. Doubt unites them." Doubt is the function of being unsure about a given proposition and therefore not willing to die or kill for it. How quickly peace among men could flourish, if we could only admit our own ignorance.
It is humility (an actual virtue) to know the limits of man's knowledge. It is noble to admit those points of which he is ignorant, and it is brave to face this mysterious world as a man of doubt. It would seem then, that the path to doubt is the virtuous one, a path found only through honest questions, and an open mind.