The Emperor was punishing House Harkonen for the decline in the spice production and was able to allocate resources among the Houses. House Atreides was a threat to the Emperor based on his own Navigators and soothsayers, so he believed by "rewarding" House Atreides he would allow a natural fight to arise and exterminate the threat.

Remember, I read it more than forty years ago, so I'm working from memory.