Because if they had to pay the same tax rate it's possible that the person who bought their house for $50,000 and can now sell it for $1.6 million might have to move and pocket their $1.55 million profit. Better to put the tax burden on the people already struggling to afford a home, kids, etc.
Then people say 'well the new purchasers are rich, they can afford it!' without thinking of the fact that their housing policies have made it so only the rich can buy a house at all. Household income to be able to afford a home in San Diego is now ~$200,000, which is well over double the actual median household income for the area. Most people have just given up on ever buying a home there or they are waiting on relatives to die to give them enough money to do it. NIMBYs have killed the idea of home ownership for the average person.