does chess.com discriminate against russia

You are confusing "A flag is a political symbol" with "A flag is only ever a political symbol."  The second may not be true, but the first is widely acknowledged.  It's true that flags can be used by different people in different ways -- they're not stable, univocal political signifiers.  And sure, it does have simple classificatory value in some cases.  But to pretend that a flag does not also often carry polical significance is simply to deny the way the world works.  Many institutions have therefore felt it's appropriate to hide the Russian flag on accout of Russia's actions.  You may not disagree with this decision -- perhaps you think these institutions are being too hard on Russia, or perhaps you even think that Russia is in the right.  Those would be intellectually coherent reasons for objecting (they're reasons I would strongly disagree with, but that's beside the point). But to pretend that it shouldn't be done because a flag never holds political meaning is risible.

Mods will be here any minute 

Of course its ok to kill a million innocent iraqis citizens in repayment for only 5000 American deaths caused by a religious group