Scheduled flights
As the FSB (successor to the KGB) will be the ones managing the FAN-ID scheme, I have no doubt that the Russian authorities will have plenty of information on who is entering the country and be able to pick off any troublemakers quickly.
However, FIFA will want to have fan zones in each city and generally make it possible for those without tickets to enjoy the atmosphere outdoors - I doubt they want something quite as controlled as the FSB would like. In any case this is Putin's chance to present Russia as a normal country rather than an authoritarian one. Boosting tourism in regional cities for the long term will also be on the minds of organsiers. Thus it is probably in Russia's interests to make scheduled flights possible subject to having complied with either a visa or the pseudo visa called FAN-ID