You're giving the quote a bizarre and implausible reading. Of course that Reagan (if he really said this) meant it to imply that a marine does make a difference, and a positive one. Any normal person interpreting the quote in good faith would make that assumption, whether or not they agree with the premise.

(Besides, googling for the source of this quote, I can't find any reference to a concrete time and place where it was uttered, nor to the rest of the speech or dialog whose part it was. This strongly suggests that it might be apocryphal, though of course I can't conclude this with certainty.)

If the quote instead concluded with "The Marines verifiably know they do make a difference." 

Then it would say the same thing but say it poorly. That this ending even occurred to you as you read the quote should be treated as evidence that this is what was meant. It is a common and highly effective rhetorical technique to leave a key element implied rather than explicitly stated. Stating it explicitly undermines the rhetorical impact. We might compare it to explaining a joke, which kills the joke. 

But as it stands the quote just says the Marines no longer wonder about this, and presents it for a good thing.

You're misreading the quote by assuming that it did not leave a key element implied.

I was thinking that it could be interpreted as the Marines knowing they don't make a difference. It reminds me of this quote:

Dr. Nefarious: "To think, they called me insane, Lawrence. We'll see who's insane when my [mutant armies] have exterminated all life on this miserable planet!"

Lawrence: "That should clear things right up, sir."

To generalize, that quote is part of the same philosophy that thinks faith better than agnosticism, belief better than unbelief, certainty better than uncertainty -- regardless of whether the evidence justifies such or not.