1. No one claims the army is short on manpower. That’s not an issue.
2. Israel has a serious demographic “time bomb” and many hilonim hope that after spending three years in the army at ages 18-21, many hareidim will chose to follow a “normal” lifestyle, thereby eliminating the threat of hareidim becoming a dominant group in Israel. The whole idea of zionism is to build a “modern” secular state, and that isn’t possible unless something can be done to reduce the number of hareidim. If hareidim keep having large families, and if only a small number go “off the derekh” (and many non-hareidim become baalei tseuvah), the zionist dream is dead.
3. For those who see Torah and Mitsvos as the basis of being Jewish, the yeshiva students are bearing the burden of national survival, giving up much parnassah to learn frull time, whereas the hilomim are deadbeats contributing nothing to Jewish survival.
4. Even if you ignore a gemara that says that if the malchus wants to call you to the army, and you are learning, you can use lethal force to defend yourself – some people hold that establishing a secular Jewish state, which rejects Jewish law and tradition as its basis, is not only not required by halacha, but is in fact prohibited. If that is the case, we are the “rodfim” and the Palestinians are the “nirdafim”, and we are prohibited from killing them or destroying their property meaning service in the IDF is prohibited. In the past people with these views, who may be a fairly high percentage of the hareidim community, have not needed to confront the zionists since they were exempted from the army by claiming they were in yeshiva (the Israelis require very little time in Beis Medrash to be a full time student – most Baal ha-Battim spend close to the required time even if they don’t aspire to be Bnei Torah).