Validation via Javascript does not work

Take a look at your code, should have something else affected this behavior.

Another thing, there is no need to change visibility and display. Only the display is sufficient.

Look at this code that I did for example.

Only the display has already worked.

<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script><linkhref="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" />
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script><inputtype="text" id="input" />
<div class="alert alert-danger" id="valida_pergunta" role="alert" style="display: none;"><span class="glyphicon glyphicon-info-sign"></span> Preencha o campo Pergunta</div>
<button onclick="validar()">VAI</button>

<script>
  function validar() {
    var input = document.getElementById("input").value;

    if (input == "") {
      document.getElementById("valida_pergunta").style.display = "inline";
    }
  }
</script>

UPDATE

As chatted in chat, it was identified that there is no action preventing the submit.

To solve this, let's follow best practices and run all of our JS when the DOM is ready.

For this:

window.onload = function(){
      //Código aqui
}

First thing to do is to have access to the button and the form, so we'll create two variables:

var button = document.getElementById("enviar");
var form = document.getElementById("form_pergunta");

(Do not forget to put the id="send" it in the HTML button)

With access to this, we can perform a function every time the button is clicked, for this we will use the addEventListener() on the button and put the following logic: CASE THE VALIDATE FUNCTION RETURNS TRUE, GIVE A SUBMIT NO FORM .

button.addEventListener("click", function(e){
    if(validar(form)) form.submit();
});

Now let's look at the validate function. This will get a parameter that is the very form we retrieved above.

function validar (form_pergunta){ 
 var pergunta = form_pergunta.pergunta.value; 
 var resposta = form_pergunta.resposta.value; 
 var desafio = form_pergunta.desafio.value; 
 var passou = true;
 if(pergunta==""){ 
  document.getElementById("valida_pergunta").style.display = "flex"; 
   passou = false;
 } 
 if (resposta == "") { 
  document.getElementById("valida_resposta").style.display ="flex"; 
  passou = false;
} 
if (desafio ==""){ 
  document.getElementById("valida_desafio").style.display = "flex"; 
  passou = false;
}
return passou;    

}

That way it should work.

I hope I have helped.