No need to make this more complex. Its really simple. Russia was anti-Hillary. Thats it. ANYONE that's not named or tied to Hillary is going to have their support.
Between her SOS office, the Obama admin that she worked under, and her foundation; she was pushing for the Ukraine revolution, was accused of funding protest movements in Russia, and her crew was going extra hard on the Magnitsky Act.
Thats why she was targeted. Putin admitted as much well before the 2016 election cycle even kicked off.