Because Robert’s (and Jon Arryn’s) policy was not to dispossess loyalists who had shown sense and bent the knee – as the Rykkers did, in the end – so that he could take their land and redistribute it. In the main, the policy was to secure the peace by guaranteeing the status quo ante bellum in return for loyalty.
Why were the Rykkers left in charge of Duskendale? Given how they were notably loyal to Aerys, and also installed by him after his first notable act of madness, it seems like taking Duskendale from them wouldn’t be too controversial, and it would be a decent seat to give away at a later date to someone who earned it.
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