The fief of Arrakis passes around the Great Houses every once in a while. The Harkonnens had it, I think, for eighty years. However, at least the pretense of the Harkonnens not being able to meet their spice quotas was used as an excuse.
Outside of the plot between the Emperor and the Harkonnens, I recall no reason or excuse for it being given to the Atreides in particular though.
EDIT - just recently read Dune - Heir Of Caladan. Set immediately before the events of Dune, this seems to add extra information, but also goes against (it seems) what is established in Frank Herbert's lore.
In it, Duke Leto infiltrates a terrorist cel which threatens the entire Imperium. He seeks to stop it from within, and dispatches his aide Gurney Halleck to the Imperial Court in order to tell the Emperor about his plans without arousing suspicion. The Harkonnens, however, capture Gurney in transit, discover the message, and withhold it from the Emperor.
Upon finding out about this, and that the Harkonnens also skimmed some of the spice to sell privately, the Emperor gives the Harkonnens a very public dressing down, stripping them of the fief of Arrakis while granting it to Duke Leto as a reward. However, he does note that the Atreides have risen in popularity, especially after Duke Leto risked his life to bring down the terrorists, and that this is a concern, concluding that he can "play the Atreides and Harkonnens against each other".
However, this happens seemingly mere days before the events of Dune, giving little time to set anything up, and the Emperor truly does seem to display hatred towards the Harkonnens - hardly conducive to jumping into bed with them.