Unfortunately for many religious ideas, in societies and cultures that have well-learned the importance of relying on evidence and cogent production and distribution of such, these "spiritual beliefs" do end up looking like irrational positions being held. And until there is sufficient evidence backing claims made of such extraordinary measure there will really be no reason for anyone who already thinks they are irrational to think differently.
Think about the initial serious/public presentation of the idea that the world was round. This was an extraordinary claim at the time, but the maker had good, solid, empirical evidence that they could produce to anyone who was capable of understanding. And so, those who didn't understand got angry, because the "round earth" challenged some of their long-held beliefs and scriptures, and because they couldn't understand the evidence, or refused to, they sought to discredit or even harm this person. Once enough people got their minds around the evidence, and more ideas for how to present this to the "layperson" were imagined and employed, then it became the more common knowledge that the Earth was round. And now it is those still claiming the earth is flat that must produce evidence to convince the majority... except that their evidence remains ever in a terrible and insufficient state - because the flat Earth simply isn't real, and so doesn't follow the patterning and modeling of reality. Hmm... interesting that... sounds familiar, doesn't it?
Anyway - you could try to make this an analogy to theism/atheism, whereby you put the theist in the position of the round-earther, and claim that it will only take finding the right evidence to make all the current deniers change their minds. And that would, honestly, do the trick in the vast majority of cases! However, expecting to be believed before you get to that point of evidence, just because you have feelings for the idea, isn't going to work.
Finally, atheists aren't in the business of actively harming anyone who presents an extraordinary claim and tries to provide evidence for it. You're more likely to simply be told that you aren't believed, or, perhaps, that you are being irrational. This is only the normal dissemination and back-and-forth discussion of ideas that we language-endowed humans have been engaging in for thousands of years now. Some people have the belief of others on their side, and some others have not. Some have good evidence, and some have not. Just because you find yourself in the "have not" bunch does not mean you are being "hurt" by those who tell you so.