A monad is just a monoid in the category of endofunctors, what's the enlightenment?
This answer may not be exactly what you are looking for. That is, I think perhaps the importance of this characterisation is being overemphasised here. The quote

a monad in X is just a monoid in the category of endofunctors of X

is originally from Mac Lane's Categories for the Working Mathematician, where it appears as a helpful intuition for the definition of monad, which, alone, can seem quite unfamiliar at first. By characterising it as a monoid in a particular monoidal category, the reader is given an alternative perspective. Note that the chapter on monads actually comes before the chapter on monoidal categories: the remark is intended to be helpful, rather than precise (it is made precise only later).
The quote was then rephrased in James Iry's infamous article Brief, Incomplete and Mostly Wrong History of Programming Languages.

A monad is just a monoid in the category of endofunctors, what's the problem?

Presented out of context, as it is in the article, it is meant to amuse. The quote has since become a meme in the functional programming community, primarily because it is amusing, rather than a key insight for functional programming (though it does also serve to pique the curiosity of functional programmers, drawing them into the wonderful world of category theory). My view is that this characterisation, while helpful and interesting, is not as important as one might imagine from its popularity.
However, this is not to say there is no insight to be gained from this characterisation. First, let me point out that, while the presentation of a monad with a multiplication and unit is clearly suggestive of a monoid, as you point out, the Kleisli presentation, with a bind and return operation, is not. It is the Kleisli presentation that is common in functional programming, so certainly the characterisation as a monoid is more interesting from this perspective.
From a theoretical perspective, one of the insights is indeed that many natural structures in computer science (and mathematics) are monoidal. From the perspective of monads (particularly with their relation to cartesian operads and Lawvere theories), monoidal structure corresponds to substitution structure (equivalently, composition structure). Substitution is ubiquitous in computer science (for example, capture-avoiding substitution in a type theory, or grafting of trees). Monads are just one more example.
While understanding formally the statement in question may not be enlightening, I suggest that it is enlightening to understand the different perspectives on monads, as it allows you to see the different ways in which monads might be used (e.g. as containers, describing algebraic structure, describing multi-compositional systems, etc.). It can be hard to appreciate just how often they pop up without having seen the different lights in which they can be seen. In this sense, monads as monoids is just one perspective (and probably not the most enlightening).
Finally, while monads themselves are inarguably very useful in pure functional programming generally, I'm not sure the perspective as monads as monoids is helpful per se. I think the Kleisli perspective, which happens to be equivalent, is the most enlightening perspective here.
In summary, this response may be a little disappointing: I don't think that understanding this relationship is all that helpful or enlightening practically (i.e. for programming). However, it is a useful perspective to keep in mind, along with the others, when considering monads theoretically.