In Rabbi Hoffman's original article arguing that yeshivah students should not serve in the army, he only referenced Gemaras that condemned the drafting of Torah scholars. Note that these Gemaras did not specify the reason why it is wrong to draft Torah scholars. Indeed, there are a number of possibilities.
When, however, it was pointed out that these Gemaras speak of talmidei chachamim, and thus presumably refer to talmidei chachamim, Rabbi Hoffman switched to a different Gemara, which was eagerly taken up by Rabbi Menken. The Gemara that they switched to was one stating that "The rabbis do not need protection" (and they argue that Rav Moshe Feinstein used this to demonstrate that yeshivah students should categorically not go to the army - later we shall see that this is far from clear).
At first, I didn't realize that there had been a switch. But as soon as I realized, I submitted the following comment to Cross-Currents:
It is surely obvious that the Gemara does not mean that yeshivah students or even rabbis are immune from harm against the Arab threat. (I hope that pointing out this obvious fact will not mean that you will accuse me of saying that Torah=chess.) Do I need to remind you of the massacres at Chevron and at Mercaz HaRav? How about the fact that Beitar and Kiryat Sefer, towns that are full of Bnei Torah, need and request army protection? Obviously, then, in the face of the Arab threat, the yeshivah students and rabbis DO need protection. In which case, we are back to the issue of why it is fair for them to demand that only other people provide it.
The Teshuvah seems to be addressed to someone who was questioning the propriety of taking advantage of the draft exemption for those that learn in a Yeshiva instead of serving in the IDF. Rav Moshe appears to allow this exemption for two reasons:Thus, not only is the Gemara not saying that yeshivah students should automatically be exempt from the draft, and not only does Rama make it clear that there is no reference here to yeshivah students - even Rav Moshe Feinstein is not necessarily saying that yeshivah students should automatically be exempt from the draft.
A) We see from the Gemara in בבא בתרא that learning can take precedence over protecting the city.
B) Israel has recognized the importance of learning Torah, and thus exempted those that learn in a Yeshiva.
The Teshuvah does not address the following issues:
1) The Teshuvah does not imply that the learning provides protection for others. Nor does it claim that learning in a Yeshiva is enough to protect oneself from the threats facing Israel at any given time. It merely asserts that while protecting the country is a very important matter, learning Torah is even more important, so that taking advantage of a draft exemption is a moral choice. The evidence is that one may exempt oneself from sharing in payment for the protection of the city. Presumably, this would not be a valid choice for someone who merely had enough money to pay for private protection. He mentions at the end of the Teshuvah his desire that the action should be a Berachah and Haganah for Israel, but this is not the basis for the p'sak.
The Teshuvah doesn't even imply that those learning in a Yeshiva are providing protection for themselves; it is hard to imagine the country being threatened militarily or with terrorism and those who learn being automatically protected, as could be the case with burglars in a city. As has been pointed out by others, even those who learn, rationally vacate vulnerable areas when they are under active attack, and so admit that this protection does not apply even to themselves in this instance.
2) The Teshuvah does not address itself to the question of what level of exemption should be provided by the country. It is addressed to the morality of even accepting an exemption given that the country permits it. It makes no claim that the existing level of exemption must remain static forever. It also does not address evasion of the draft in opposition to the laws of the country.
3) The Teshuvah is not completely silent on the level of dedication or achievement needed to justify an exemption. It actually mentions that one can accept an exemption to become גדול בתורה ובהוראה וביראת שמים. Note the reference to becoming a Posek, not merely someone that learns. Presumably, not everyone who learns in a Yeshiva is material for becoming a Posek.
Rabbis do need protection from the Arab threat. (Similar to how Rabbi Menken needs protection from comments that undermine his argument.) It is unfair (as well as lacking any clear source in Chazal or the Rishonim) to demand that this protection be provided solely from people outside the charedi community. Indeed, this point is made explicitly in an early responsum from an early Rav Moshe: "Shall your brothers go to war, while you remain here?"