There are three distinct issues.
One is Bitul Torah -that would apply even if you are no so frum as to have problems in the army, and totally support zionism.
The second is the “spiritual” danger which is a polite way of saying that army harasses frum soldiers and persecutes them if they are too frum (e.g. gives you a choice between davening with a minyan or having breakfast) with the hope that the soldiers will lower their level of observance and become more normal – this can be mitigated in several ways, including having special “segregated” frum units.
The third is the belief that the state is treff, i.e. there is no halachic basic for the zionists to have seized control from the Arabs and therefore we are the agressors and we have no right to kill the Arabs in defense of what is little better than theft, and certainly there is no basis to be bitul Torah or to put up with harassment in order to help defend the zionist state.