There are many different definitions of "humility," so this question cannot be answered without first defining what kind of humility is to be valued at all.
I value only one kind of humility, which is close to that defended by Kant. In Kant's view humility is the maintaining of a correct and accurate self-opinion, which must necessarily include self-acknowledgment of your inevitable fallibility, and all of your limitations (including actual degree of ignorance or uncertainty in any matter of knowledge), and the appropriate state of deference (e.g. apologizing when you have done wrong or been in error, and not blaming others for your own mistakes; deferring to the superiority of others when it is genuine and appropriate; etc.).
This kind of humility is set in contrast to arrogance and self-presumption, whereby one thinks more of oneself that the facts merit, such as claiming you are more capable than you are, or more knowledgeable than you are, or more infallible than you are, or more important than you are, or more deserving than you are, or more privileged than you are, and likewise any other self measure. But this means feigning a state of inferiority is not a virtue but another form of deception (if you know it is untrue) or delusion (if you erroneously believe in your inferiority), and thus calling such states "humble" is a pejorative and not praise--except in cases of moral deception (as when a slave knows he is not inferior to his master but must pretend to be for his own welfare and the welfare of those he cares about, then calling such a slave "humble" is just a value-neutral description of his behavior).
Humility in this sense is of great value in the naturalist worldview, because it follows necessarily from the naturalist's supreme value placed on the truth (both telling the truth and having true beliefs), and because the overall net consequences to one's happiness of either excessive or insufficient humility are negative and thus self-defeating. Which is the same reason the truth is valued: it is better to your happiness overall that you cultivate the habit of loving, speaking, and seeking the truth (and thus being constantly vigilant to detect and correct your own errors), and then developing the means to cope with and make the best of that truth, than to try and gerrymander a way of life that depends on maintaining or repeating some degree of deception or self-deception.
When others allow you to be honest, you are always happier, and when you allow yourself to be honest with yourself, you are even happier still. And with true beliefs you will always be more successful, realistic, or efficient in achieving your goals. And with a love of the truth maintained across the board you will more reliably detect and correct your own errors, which entails eventually detecting and correcting errors of countless kinds that, left undetected, would substantially undermine or hinder your happiness.
Other kinds of humility may be valued by other naturalists. But I take quite the opposite view on such things as false modesty, self-abasement, or unconditional restraint from contempt and ridicule, which are all hindrances to human happiness, not aids to it. Ridicule, for example, is an essential component of social expression (it is how we punish the ridiculous, and thus why we have comedy and why it is so effective an agent of social change); self-abasement is an invitation to exploitation; and false modesty is simply lying, which either causes harm or confusion, neither of which is very helpful to anyone.