The difference is this; Theology is not akin to astrology or the exegesis of Harry Potter novels - it is a study undertaken by serious people. Many of the foundational figures of the rationalism that Dawkins privileges were also deeply interested in theology - Descartes, Kant, Rousseau and so on. If people you respect in one area also appear to have a deep interest in something else, then it would seem to be the least one could do to pay the tribute of respecting that pursuit as sincere and un- ephemeral. Anyone who reads Augustine or Origen or Aquinas - or more modern philosophers of religion such as levinas or Marion - will grasp immediately that, whatever the validity of the ultimate claims, we are in the presence of real thought.
Works such as Dawkins - and that of even more egregious figures such as the silly AC Grayling - play a loose game, equating a 'common sense' idea of rational with its philosophical counterpart, and assuming a match between the two. Actually, it is extraordinarily difficult to work out any definition of reason that isn't simply tautologous - and reason is of no more help in saying anything useful about 'truth' - as opposed to 'facts' - than religion.