The Daleks were engineered to believe that universal domination was their purpose & their entitlement ("Genesis of the Daleks"). They would (and do) hate anyone who obstructed that. Nobody has done more to obstruct it or has obstructed it more often than the Doctor has, and as such they consider him their main enemy due to his many encounters with them over the years. More recently, of course, the Doctor is known as the man who attempted to destroy the entire Dalek race to end the Last Great Time War, adding to their hatred of him ("The Parting of the Ways"). Note that this is one event that did still occur, despite the Doctor managing to find a way to avoid destroying the Time Lords in "The Day of the Doctor".