The primary reason is that Merryman represents an opinion/ruling by a solitary member of the judiciary, aimed at the President (the President representing a co-equal branch of government with the Judicial Branch). Lincoln's ignoring the ruling falls into a class of acts called "Presidential Acts of Constitutional Interpretation." Lincoln was not the first President, nor the last, to ignor court rulings aimed at the Presidency. Besides Merryman, one could look at Andrew Jackson's refusal to enforce Worchester vs Georgia, 31 US 515 (1832). More recently, Richard Nixon refused to abide by lower court rulings, until threatened by the third branch of Government with impeachment.
There are several other factors that weigh against Merryman. (1) It has not been incorporated into statutory law. (2) It was not accepted by other branches of government. (3) It was the opinion of a lone judge and was unsupported by the US Supreme Court. (4) It was partisan in nature. (5) The act of ignoring the ruling has been supported by history and has itself been precedent setting. (6) It has been eclipsed by other rulings.
Unlike Ex parte Milligan (1866), which has established precedent, the Merryman case is usually only studied as part of history. Indeed, the case is recalled when discussing "the Merryman power of the Presidency." It has ramifications today. When a President commits US troops to conflict in an emergency, without having had time to consult the Congress, or obtain from the a declaration of War, the authority to enforce all aspects of US law is based on the principle of the President's power of constitutional interpretation.
I need to confess, that much of this post is not my own. I have been coached by a lawyer friend of mine who pulled out some of her old law school notes. I am also made aware of a recent book entitled the "Merryman Power and the Dilemma of Automous Executive Branch Interpretation." I'm going to try an find it, if it is still in print.
From Milligan:
It is claimed that martial law covers with its broad mantle the proceedings of this military commission. The proposition is this: that in a time of war the commander of an armed force (if in his opinion the exigencies of the country demand it, and of which he is to judge), has the power, within the lines of his military district, to suspend all civil rights and their remedies, and subject citizens as well as soldiers to the rule of his will...If this position is sound to the extent claimed, then when war exists, foreign or domestic ... the commander of one of them can ... substitute military force for and to the exclusion of the laws, and punish all persons, as he thinks right and proper, without fixed or certain rules.
The statement of this proposition shows its importance; for, if true, republican government is a failure, and there is an end of liberty regulated by law. Martial law, established on such a basis, destroys every guarantee of the Constitution, and effectually renders the "military independent of and superior to the civil power."
The Constitution of the United States is a law for rulers and people, equally in war and in peace, and covers with the shield of its protection all classes of men, at all times, and under all circumstances. No doctrine, involving more pernicious consequences, was ever invented by the wit of man than that any of its provisions can be suspended during any of the great exigencies of government.