A monopolist can earn positive profits in the long run because it has market power, allowing it to charge a price that is higher than marginal cost.
In the case of a natural monopoly (i.e. a firm whose average cost decreases as output increases due to large fixed and low marginal costs), the government should generally regulate the monopolist to charge a price equal to marginal cost.
A monopoly with a more elastic demand curve will have more market power.
Patent protection essentially gives software developers a monopoly; therefore, the practice of granting patents to developers should end.