There was a spark between the Doctor and Kes only a fool could ignore.
Neelix was impossibly Jealous of what his girlfriend was up to with almost everyone, yet this computerized creature occupied half her day sometimes and our favourite Kitchenrat never suspected that some tryst might have germinated?
In retrospect Neelix must have periodically stuck his (metaphorical) hands into the Doctors programing and cleaved out this holograms ongoing romantic feelings of love for the adorable little Ocampan refugee.
It's a machine.
There's no guilt.
Barely a crime.
Ditto for Seven of Nine guarding her own virtue from the lusty digital surgeon.