Hardly nonsense, and hopefully neither we, nor others from beyond Earth, will ever be "beyond it."
I have no problem with spirituality, but I consider organized religion nonsense and hope we will move beyond that.
I'm also against a chaplain aboard federation ships, it's not just an international crew, it's an interplanetary crew, there are too many faiths and belief systems for it to work. A counsellor can do the job much better than a chaplain who is clearly a member of a specific belief system, of course the counsellor can have a religion too, but they're not part of the job description.
Imagine a bajoran vedek having the chaplain job on a ship, could someone from earth relate to him? After all his "gods" are real, you can literally visit them, there's no doubt that they exist, even if you consider them to be just wormhole aliens, you know they are real. There's a very big disconnect that's not comparable to christians and muslims for example, as those religions are basically identical.
Of course a bajoran counsellor would most likely have the same faith, but it's just not as obvious.