A boycott isn't just about making a difference (though SU killing some TLV frequencies would be a win), it's about taking a principled stand for what's right.
They don't have much competition on that route. And if they feel it's important enough not to concede, they'll pay the economic price even if they have to fly half empty or at cut throat prices.
As for principled stand, did you ever boycott Amazon over Bezos funding a campaign to legalize same-sex marriage in Washington state? Do you boycott KIND over what Lubetzky funds with his money?
I personally have no problem with AEROFLOT (though connecting in Moscow without an entry visa is always a risk of unpleasant things happening), Amazon is too big and easy to use for me to boycott (and no one would even know), but I refuse to buy any KIND bars, profits of which fund projects that try to undermine Jewish existential interests.