How can beliefs held by half or more of the population be considered deviant?

When a specific belief is held by more than half of a population, then such belief is being held by the majority of the population, which goes by the "half plus" formula, or its dictionary definition:

an amount that is greater than half of its total. 

Still, the common belief is that, if the majority believes a norm or belief, it is universally accepted as a rule to abide. This is not always the case.

The answer, therefore, is that a belief can still be considered deviant, or against the collective norm, even when the majority of the people believes in it, when a faction, or 

a group within a larger group that has different ideas and opinions than the rest of the group

is also in charge of deciding the collective social norms by which a given population will abide. 

These factions are ruled by people who are influential and powerful, whether they represent the interests and beliefs of the majority or not. They can be anybody: book editors, politicians, actors, community representatives, artists.

As long as these people hold the power to influence with what they write or say, they may APPEAR to be the majority, when in fact they are just have a greater influence than members of the majority. As such, their publications, speeches, books, and laws can appear to be "the rule." 

This is how the beliefs of the majority, or "half plus" of the population, may still be considered deviant. If the smaller group is more influential and has the power of laying down the law, they can call out the majority as "wrong" and call themselves and their agendas "correct." Sadly, the same majority that becomes disenfranchised by the influential faction also allows this to happen. 

Now, on a side note, let's be very careful with the word "deviant." A deviant is not necessarily a bad person, or someone who is rebellious or challenging. For all I know, I am a deviant because I celebrate Day of the Dead, instead of Halloween, in a country where Halloween is the second most awaited celebration. 

A deviant is simply someone who thinks or acts in a way that detours, or deviates, from the norms that those factions have established as rules. 

Again, since rules and norms are actually determined by SMALL groups, and not by the majority of the population, celebrities such as Ben and Jerry, of the ice cream fame, consider that maybe the deviants are those who make the norms, being that they are the smaller fragment of the population, in terms of numbers. That, however, is another story. Yet, it helps us see how this issue with who establishes the rules can be seen from different perspectives. 

Therefore, the issue of influence can happen with any common belief, from creationism, to the paranormal, to who would make the best US President, to who killed JFK. As long as a small, powerful group holds the reigns of public opinion and social influence, their thoughts will SEEM to be as "normative" when, in fact, they are not. As such, the beliefs of the majority will be considered deviant.