The primary reason that natural monopolies are allowed to exist in areas such as energy production is that

Monopolies are allowed in areas such as energy production because IT IS MORE EFFICIENT TO ALLOW ONE COMPANY TO BE IN CONTROL.
This type of monopoly is called natural monopoly. Natural monopoly occur when the most efficient number of firms in an industry is one. In this case, the cost of producing the product is always quite high, so the practical thing to do is to have only one company produce that good. 

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