Did you actually READ the report. If you had, you would know that it made NO sweeping comments about "our troops." What is said was (and I quote):
Disgruntled Military Veterans
(U//FOUO) DHS/I&A assesses that rightwing extremists will attempt to recruit and radicalize returning veterans in order to exploit their skills and knowledge derived from military training and combat. These skills and knowledge have the potential to boost the capabilities of extremists—including lone wolves or small terrorist cells—to carry out violence. The willingness of a small percentage of military personnel to join extremist groups during the 1990s because they were disgruntled, disillusioned, or suffering from the psychological effects of war is being replicated today.
— (U) After Operation Desert Shield/Storm in 1990-1991, some returning military veterans—including Timothy McVeigh—joined or associated with rightwing extremist groups.
— (U) A prominent civil rights organization reported in 2006 that “large numbers of potentially violent neo-Nazis, skinheads, and other white supremacists are now learning the art of warfare in the [U.S.] armed forces.”
— (U//LES) The FBI noted in a 2008 report on the white supremacist movement that some returning military veterans from the wars in Iraq and Afghanistan have joined extremist groups.
Thus, it specifically refers to "small numbers" and being "targets" of radical right wing nutjobs. It is the JOB of homeland security to be on top of ANY potential threats to Americans. Unfortunately, in this day and age, that CAN include those from the VERY FEW insiders who might have an ax to grind. It is a practical reality not to be ignored.