I seem to remember when the team was being unveiled that MLSE went to great pains to explain that Toronto FC was a brand name, it wasn't a short version of Toronto Football Club, anyone else remember that? I never quite got it, but whatever.
Referring to the team as "The FCs" is stupid. But "The FC" actually does make sense if you accept that FC is short for Football Club. It sounds weird, and wouldn't be my go to (I 99% of the time go with TFC), but technically "The football club won 1-0" makes slightly more sense than saying "Toronto won 1-0". In either case more description is required (what football club? what Toronto team?), even if it is pretty obviously implied (like the Leafs will ever get a shutout with Reimer in net, or the Jays post a shut out with THAT rotation)