“My understanding is that if you want protection that you can consider Hishtadlus, the minimum of being Frum is Shomer Shabbos!”
Every Mitzvah that every Jew does counts – and counts tremendously. Not doing one Mitzvah doesn’t take away from the fact that you are doing another Mitzvah. If someone speaks Loshon Hora, his keeping Shabbos still counts, and if someone else is careful not to speak Loshon Hora or to keep kosher, those things count even if he doesn’t keep Shabbos.
If someone puts on Tefillin once in his life, it is a Mitzvah. If the government grants exemptions to Yeshiva Bochurim, they are doing a Mitzvah. In fact, I think a certain Gadol may have said that it is in that zchus that they have protection from Hashem (and no, that is not zionism – it doesn’t mean the government should have been created in the first place, but any Mitzvos they do still count despite any aveiros that they do.)