In an era and sport where waving a national flag has far more to do with player identities than with national politics (see: the coming lack of Ukranian flags at the San Siro), this incident underscores a couple of things where an event like the WC can play a role.
On the one hand, you have trigger-happy people who will jump at any opportunity to intepret someone's expression of familial or club allegiance as an overt endorsement of human rights violations. Sorry to say, but that's one big DUH. An incident like this holds up a mirror to those who make no attempt to recognize the right for pluralist societies to exist -- and these people can show a great intolerance for anything other than their own way of life and own way of thinking.
On the other hand, I appreciate the fact that the World Cup provides a true world stage. That the whole world can witness goal celebrations with bows to Mecca in the world's grandest sporting stage shows that the pluralist question goes for
everybody. And while it would be simplistic to say that there are those who view everything in the world through Israel-or-Palestine-tinted glasses, and they need to get over themselves and recognize that other realities exist beyond their own narrow thinking ... it also goes that it's a bit clueless and culturally insensitive for an Israel flag-waver to think that there won't be people who will interpret that as some sort of political statement.
Hey, we have people waving Mexican flags at U.S. rallies in support of more liberal immigration laws.

Which is clearly their right to express how they feel personal solidarity to a cause. But at least try to get a clue as to how others will interpret it. It may not stop you from doing it, but at least do what you can to not be all dumbfounded by the reaction from some circles. It really isn't brain surgery to get clued in about the world on such a visible level.