You often hear it said that "museums of art are our new churches": in other words, in a secularising world, art has replaced religion as a touchstone of our reverence and devotion. It's an intriguing idea, part of the broader ambition that culture should replace scripture, but in practice art museums often abdicate much of their potential to function as new churches (places of consolation, meaning, sanctuary, redemption) through the way they handle the collections entrusted to them. While exposing us to objects of genuine importance, they nevertheless seem unable to frame them in a way that links them powerfully to our inner needs.

The problem is that modern museums of art fail to tell people directly why art matters, because modernist aesthetics (in which curators are trained) is so deeply suspicious of any hint of an instrumental approach to culture. To have an answer anyone could grasp as to the question of why art matters is too quickly viewed as "reductive". We have too easily swallowed the modernist idea that art that aims to change or help or console its audience must by definition be "bad art" – Soviet art is routinely trotted out here as an example – and that only art that wants nothing of us can be good. Hence the all-too-frequent question with which we leave the modern museum of art: what did that mean?

Why should this veneration of ambiguity continue? Why should confusion be a central aesthetic emotion? Is an emptiness of intent on the part of an artwork really a sign of its importance?

Christianity, by contrast, never leaves us in any doubt about what art is for: it is a medium to teach us how to live, what to love and what to be afraid of. Such art is extremely simple at the level of its purpose, however complex and subtle it is at the level of its execution. Christian art amounts to a range of geniuses saying such incredibly basic but extremely vital things as: "Look at that picture of Mary if you want to remember what tenderness is like"; "Look at that painting of the cross if you want a lesson in courage"; "Look at that Last Supper to train yourself not to be a coward and a liar". The crucial point is that the simplicity of the message implies nothing whatsoever about the quality of the work itself. Instead of challenging instrumentalism by citing the case of Soviet art, we could more convincingly defend it with reference to Mantegna and Bellini.

This leads to a suggestion: what if modern museums of art kept in mind the example of the didactic function of Christian art, in order once in a while to reframe how they presented their collections? Would it ruin a Rothko to highlight for an audience the function that Rothko himself declared that he hoped his art would have: that of allowing the viewer a moment of communion around an echo of the suffering of our species?

Try to imagine what would happen if modern secular museums took the example of churches more seriously. What if they too decided that art had a specific purpose – to make us a bit more sane, or a little bit wiser and kinder – and tried to use the art in their possession to prompt us to be so? Perhaps art shouldn't be "for art's sake", one of the most misunderstood, unambitious and sterile of all aesthetic slogans: why couldn't art be, as it was in religious eras, more explicitly for something?

Modern art museums typically lead us into galleries set out under headings such as "the 19th century" and "the Northern Italian School", which reflect the academic traditions in which their curators have been educated. A more fertile indexing system might group together artworks from across genres and eras according to our inner needs. A walk through a museum of art should amount to a structured encounter with a few of the things that are easiest for us to forget and most essential and life-enhancing to remember.

The challenge is to rewrite the agendas for our art museums so that collections can begin to serve the needs of psychology as effectively as, for centuries, they served those of theology. Curators should attempt to put aside their deep-seated fears of instrumentalism and once in a while co-opt works of art to an ambition of helping us to get through life. Only then would museums be able to claim that they had properly fulfilled the excellent but as yet elusive ambition of in part becoming substitutes for churches in a rapidly secularising society.

• Alain de Botton is founder of The School of Life and the author of Religion for Athesists. He will present a Sunday Sermon The School of Life on Religion for Atheists on Sunday 22 January at Conway Hall, WC1