Chuck Hagel survived the nomination process, but many problems still lie ahead.

Hagel’s nomination as secretary of defense was not well received by most Republicans. And his performance during the confirmation hearings did nothing to help his cause. In the end, the nomination narrowly squeezed past a cloture vote. More than a few in Hagel’s old party gave him a thumbs-down in the final vote.

So while Hagel has settled in at the Pentagon, he cannot sit easy. He is a marked man. His critics will be looking for the first misstep to call for his head. The new secretary also faces a new problem—a possible half-trillion dollars in defense cuts on top of the approximately half-trillion dollars in cuts he inherited. Hagel may be efficient, smart and prudent in making the Pentagon’s ends meet. But he will still have to run a Walmart-size company on a 7 Eleven-size budget in a world that is not much safer than it was four years ago.

Still, neither budgets nor headhunters may prove to be Hagel’s biggest headache. He should be most worried about the dark shadow of sour civil-military relations.

The best take on American civil-military relations remains the introduction to Eliot Cohen’s masterful book, Supreme Command. Cohen makes the point that the realms of political and military decision-making are not distinctly separate spheres. Rather, they do and should overlap. Generals should make decisions that win battles. They shouldn’t meddle in politics, but their military advice always ought to be suitable, feasible and acceptable. During World War II, for example, the U.S. Army estimated that about 10 percent of the nation’s manpower could be put in uniform without creating a worker shortage that would undermine the capacity of industry to sustain the armed forces. It would have made no sense for the military to ask for a bigger force than the nation could sensibly field.

In contrast, political leaders should never outsource the field of battle to the field marshals. Lincoln, one of the leaders profiled in Supreme Command, quickly learned the lesson that he had to understand war to lead the nation to victory in war.

Cohen’s case study of Lincoln captures precisely how that small space shared between the military and political spheres demands the very best of leaders—both civilian and military. Operating effectively requires the right mix of trust, confidence, competence and character.

There are many signs that the bridge across the Potomac is shaky. The president has sent plenty of signals that, beyond reciting the usual platitudes, he doesn’t consider preserving military readiness and defense capabilities more of a priority than keeping any other government department humming. He was, after all, more than willing to hold defense hostage during the sequestration debate—trying to force conservatives in the Congress to choose between tax hikes or gutting national security (which takes 50 percent of the sequestration cuts on top of the billions the president has already taken off the Pentagon’s top line).

Meanwhile, the Pentagon’s top brass have a credibility problem of their own. When the former chairman of the Joint Chiefs of Staff, Admiral Mike Mullen, famously declared the national debt was America’s number one national-security threat, many in Washington interpreted the comment not as a warning to get the nation’s fiscal house in order but as green light for defense cuts. Further, the current chairman and chiefs have not been much better advocates for a strong national defense. For months, they said virtually nothing about the dangers of the so-called sequester. Only when the White House wanted to ratchet up pressure on Congress to axe the sequester in favor or higher taxes did the brass start trumpeting their doom and gloom warnings. When it comes to readiness and capabilities, the senior officer corps is starting to look a bit like presidential sock puppets.

In the last few years, senior officers striking a discordant note have been silenced pretty quickly. Take the case of the surprise early retirement of Marine Corps General James Mattis, the commander of U.S. Central Command, which watches over all the hot spots in the Middle East. “[W]hat message does it send to the services,” writes Bing West in National Review “when the one leader known for his war-fighting skills rather than bureaucratic and political talents is retired early via a press handout?”

Obama’s Pentagon is starting to look a lot like Clinton’s, where senior commanders found themselves serving a president who, never comfortable wearing his commander-in-chief hat, was more than willing to cut corners on national security. Ultimately, this leaves the armed services stuck with trying to do the best they can with what is at hand.

The saving grace for Clinton was that he had Bill Cohen as secretary of defense. Cohen worked hard to gain the trust of the chiefs, bridge the gap between them and the White House, and protect the chiefs from an increasingly hostile Congress. Whether Chuck Hagel can match that performance remains an open question.

The White House is banking on the end of combat operations in Iraq and Afghanistan, and the president’s popularity at home, to shift the focus away from what inevitably will be strained times at the Pentagon. How Hagel handles the senior armed-service leaders and how much demand there is for U.S. military force in the future may determine how well that strategy works.

James Jay Carafano is vice president of Foreign and Defense policy studies at The Heritage Foundation