Actually, many career German officers--those who had entered the service before the Nazi party consolidated its power--had little esteem for Hitler and the party and used their personal clout to make independent decisions; Rommel wasn't unique in that regard.

Wikipedia: Hitler promoted Friedrich Paulus—commander of the 6th Army at Stalingrad—to the rank of field marshal on 29 January 1943, shortly before his army's inevitable surrender in order to encourage him to continue to fight until death or commit suicide. In the promotion Hitler noted that no German or Prussian field marshal at that point in history had ever been captured alive. Paulus surrendered anyway, claiming "I have no intention of shooting myself for this Bavarian corporal".

The German view in the inter-war years was that the military should be divorced from the direct control of civilian politicians (and vice versa). The Weimar constitution forbade members of the military from holding party cards or voting; this rule was not suspended, in fact, until 1944. Numerous German officers who entered the service during that time became conditioned to that way of thinking. In keeping with this attitude: "The Wehrmacht refused to adopt officially the Hitler salute and was able for a time to maintain its own customs."

You should also consider the origins of the services and the pre-war makeup of the officer corps: many Wehrmacht and Kreigsmarine officers were Junkers--members of the Prussian aristocracy. They held a very dim view of the Nazis, since naziism began, after all, as a plebeian movement.

Although Rommel was not a noble, he came from a comfortable middle-class background: his father was a university professor and former army officer. So it makes sense that his views and loyalties would be more in line those with his traditionalist, "professional" officer peers, as opposed to the hard-line views promulgated by the Nazi party.

As an example of the Nazis' plebianism (and Rommel's disdain for some of the party's actions): "The Propaganda Department of the NSDAP re-wrote Rommel's life story, and in a 1941 article appearing in the Nazi newspaper Das Reich they presented him to the German people as a master mason's son who was an early member of the Nazi Party. Their intent was to make Rommel a "showcase member" of the NSDAP. Rommel was incensed over this false narrative (he was never a member of the Party), and complained to Das Reich. In response he was told: "Wenn es auch nicht stimme, wäre es doch gut, wenn es stimmen würde," which can be translated to: "Even if it is not true, it would be good if it were." Rommel was not mollified, and insisted on a correction. Das Reich ended up printing a retraction, placing it in a remote location."--wikipedia

The Kreigsmarine (excepting, perhaps, the U-boat service) was even more traditional/non-"nazified" in their attitudes (and conduct). The naval forces were historically liberal; It was sailors who (began the German revolution)[http://en.wikipedia.org/wiki/Kiel_mutiny] which transitioned Germany from a monarchy to a Republic. (The Luftwaffe, on the other hand, was a much newer service--built, essentially, by the Nazis--so Luftwaffe officers were more about the "party line.")

That's part of the reason the Nazis created the SS and grew the group from Hitler's personal bodyguards to a full-fledged army (the Waffen-SS) in its own right. Being party members (and officers being, ipso facto, party officials), SS troops were willing (and obligated) to follow orders without question.

So essentially, Rommel was hardly alone in the German armed forces in terms of not buying into Naziism or following purely political orders (i.e. orders which would serve no military purpose).

Of course, none of this is to say that the Wehrmacht was wholly without blame for war crimes and atrocities. They were certainly "nicer" than the SS, but plenty of enthusiastic Nazis and generally bad people put on Wehrmacht uniforms and did awful things during the war.

Wikipedia actually offers an interesting discussion of some of these issues: http://en.wikipedia.org/wiki/Nazism_and_the_Wehrmacht