The ending deliberately strengthens the sense of muddled identity rather than resolving it. Roxane says, "I loved but once, yet twice I lose my love!" And Cyrano tells her,
I would not bid you mourn less faithfully
That good, brave Christian: I would only ask
That when my body shall be cold in clay
You wear those sable mourning weeds for two,
And mourn awhile for me, in mourning him.
The point is quite deliberately not that Roxane had really loved only Cyrano all along, nor that she had really loved them both all along, but that she had loved Christian, and yet she loved Christian only in part for being Christian; in part she loved him for being Cyrano. She really did love Christian, for his beauty and for his courage; she really did love Cyrano under Christian's name, for his wit and passionate eloquence; and she had no way of distinguishing the two in the love itself. There was only one object of Roxane's love; she just didn't know that that one object was two persons.
That's the story and the idea. I want to raise it in order to raise a point about how words, like names, apply to things. We can start with asking the question: Is the implication of Cyrano de Bergerac, that the one object of Roxane's love was two people, logically coherent. One could argue in this way. If Cyrano and Christian are one object of love, they must be either a single object that is Cyrano or a single object that is Christian, because Cyrano and Christian are not the same thing. But either assumption yields a contradictory conclusion: either Cyrano is something that is not Cyrano or Christian is something that is not Christian. We could put it in other terms. Cyrano is not Christian. The single object of Roxane's love is Cyrano. And the single object of Roxane's love is Christian. Thus the single object of Roxane's love is Cyrano and not Cyrano, Christian and not Christian, a contradiction. Or again: if Cyrano is the object of Roxane's love, and Christian is the object of Roxane's love, and Cyrano and Christian are not a single thing, the object of Roxane's love cannot be a single object: there must be as many things loved as there are things that are loved.
This cold conclusion, according to which Roxane's own view of her love is irrational and incoherent, would perhaps be something we would have to accept with regret if it were really as thoroughly logical as it seems to be at first glance. In fact, however, these arguments commit the age-old fallacy of figura dictionis -- they make the mistake of assuming that the same words means the same underlying logical structures. In fact, 'the object of Roxane's love' is capable of applying to things in at least two distinct ways: it could be applied determinately or it could be applied confusedly. Taken determinately, there are two objects of Roxane's love: the individual Christian and the individual Cyrano. Taken confusedly, there is only one: Christian and Cyrano insofar as they are not distinguished (or distinguishable, as the case may be). All the arguments treat a term that obviously should be taken confusedly as if it should be taken determinately.
To see that this is not ad hoc, we need to recognize just how essential this distinction is to much of our reasoning. Suppose I say, "At least one of these soldiers is not a lieutenant." In this case, I am taking the common noun, 'soldier', determinately. Since it is a common noun, it leaves open the possibility of there being more than one soldier, but for the subject term to work as it must for this sentence to make sense, we can't be taking soldiers indeterminately: if at least one soldier is not a lieutenant, then there is some soldier, namely, this individual soldier, who is not a lieutenant; and if there are two, then this soldier is not a lieutenant and that soldier is not a lieutenant; and so on if there are three or more. But 'a lieutenant' here is not taken determinately here: it is not a claim that at least one soldier is this or that lieutenant. The term is taken confusedly. If I did take the term determinately, saying, "At least one soldier is not at least one of these lieutenants," that would be a very different claim. Likewise, if I say that "Every good dog is an animal that goes to heaven," I am not taking 'good dog' determinately. I am taking good dogs indeterminately or confusedly, making no distinction among individuals. Likewise, 'an animal that goes to heaven' is taken confusedly and not determinately: I am not saying that every good dog is this animal that goes to heaven; nor am I saying that every good dog is this or that or that other animal that goes to heaven.
In Roxane's case the confused application of the term is due literally to confusion; this is what makes relatively plausible what is the genuinely unusual (but not impossible) logical feature of the predicament, namely, that it forces a proper name ('Christian') to be taken determinately and indeterminately depending on the circumstances and that one of the major players, namely Roxane, is not in a position (until the very end) to say when it should be taken one way and when it should be taken the other way (indeed, she doesn't know until the end that it can be taken both ways, and that many things that she said of Christian, taking the name determinately for Christian, are really only true of Christian if we take the name indeterminately for Christian and Cyrano). But cases of the distinction doing real logical work in a context not depending on psychological confusion lie ready at hand in practically everything we say.
Thus Roxane's final assessment of the situation is not logically confused; and, indeed, it is exactly right.