In the case of disabled applicants, the rationale is also straightforward--disabled adults can contribute but are prevented from doing so by various structural barriers, including discrimination. The gov is helping remove such barriers to give them equal access to job opportunities and to keep them off welfare rolls.
The case of giving military veterans preferences is less straightforward. The argument for discrimination doesn't apply in an age where the military and intelligence agencies spend hundreds of millions of dollars on marketing--not just on TV commercials, but on more subtle placements such as pre-sporting game and halftime ceremonies. Mainstream movies now have fewer Full Metal Jackets and Born on the Fourth of Julys while continuing to make many pre-Vietnam war movies, reflecting not only an erasure of America's prior opposition to proxy wars but a sustained effort to link the current military with an era of defensive wars. (Perhaps I'm the only one who thinks it's odd to reach that far back in history but not introduce new movies about the Kent State student shot by the Ohio National Guard or Abraham Ribicoff.)
Additionally, if a military veteran attended college before joining the military, most likely he or she is already at a level equivalent to the average civilian applicant and doesn't need any barriers removed. If the veteran joined straight out of high school, then the government and taxpayers provided the person with vocational opportunities not generally available or trained the enlistee using taxpayer dollars. In other words, not only has the civilian taxpayer paid upfront to train the military--many of whom would otherwise lack options or who are ineligible to enroll in a competitive college--but now must compete with ex-military personnel despite not being given similar options in the civilian sector (no GI Bill, no free vocational training, etc.).
You may argue such incentives are necessary in order to have a voluntary draft, but with the advent of drones, we need fewer enlistees, not more. You may argue the enlistee is under contract once signed and sacrifices measures of freedom, but "following orders" in an age of repeatedly unnecessary wars contains no honor--and certainly not a choice that should be encouraged through debt to foreign governments. Indeed, the only reasons such a system is possible is because America directs 49% of its discretionary spending--about $500 billion annually--to act as the world's cop, a role at which it is clearly failing post-Iraq, post-Syria, post-Libya, post-ISIS, and post-Crimea. According to the U.N., a "total 65.3 million people were displaced at the end of 2015, compared to 59.5 million just 12 months earlier."
To summarize, America's military and civilian leaders have lost every war since Vietnam except for skirmishes in Panama and Grenada, and such wars have cost American taxpayers $14 trillion. It is time for voters and corporate leaders to say, "Enough. President Eisenhower was right about the military-industrial complex. I shall do nothing to assist America in falling off the cliff it currently teeters upon."
Bonus: Military Times reported in November 2016 that veterans now comprise roughly one-third of the U.S. federal workforce—or more than 600,000 positions.