The discipline took shape in the nineteenth century, alongside empire, and its early practitioners generally assumed that religions were comparable objects of the same kind, arranged on a scale from primitive to advanced with their own tradition at the top.
Both halves of that assumption have since been attacked, and the attack on the first is the more serious. Critics have argued that religion is not a neutral category found in the world but a modern Western concept, formed in specific European arguments and then exported, and that applying it to societies which drew no line between religious and other life imposes a distinction they did not make. The Sanskrit, Chinese and Arabic words routinely translated as religion do not carry the same content, and the mismatch is not a translation problem to be tidied up.
A related criticism targets the teaching shape of the field. The convention of presenting a set of world religions, each with a founder, a scripture and a set of doctrines, fits Christianity closely and other traditions less well, and it makes textual orthodoxy the standard against which practice is measured. Work on the category of Gnosticism has made the same case in miniature, showing a scholarly label assembled from disparate material and then treated as a thing.
The discipline continues, more self-conscious about its instruments. The reasonable position is that comparison is indispensable and that the categories used to compare must be argued for rather than assumed.