I completely agree that it is incorrect to equate all Jews with Israel or Zionism. However, I think one thing that works against this, is the proliferation and frequent use of phrases like 'Jewish state', and insistence on the 'right of the Jewish state of Israel to exist'.
This is the danger of quasi-theocratic countries founded on the basis of a religious identity rather than secular ideas that also tolerate various religions and show no favoritism to any one in particular. On one hand Israel wants to assert it's right to exist as a 'Jewish state'.... but then on the other hand, Jews should not collectively be held responsible for the actions of the 'Jewish state'. It's hard to determine if Israel does the things it does because it is a Jewish state, or in spite of that.
I also think it's important to point at that just as Jews should not collectively be held responsible for the actions of the Israeli government, Palestinians and Islam should not be held collectively responsible for the actions of Hamas. Yet, Israel's strategy (as stated openly by Israeli ministers) seems to be one of retribution and collective mass punishment of the Gazan population for the actions of Hamas.