At the point you are calling your function, the rest of the page has not rendered and so the element is not in existence at that point. Try calling your function on window.onload maybe. Something like this:
<html>
<head>
<title></title>
<script type="text/javascript">
window.onload = function(){
var refButton = document.getElementById("btnButton");
refButton.onclick = function() {
alert('I am clicked!');
}
};
</script>
</head>
<body>
<form id="form1">
<div>
<input id="btnButton" type="button" value="Click me"/>
</div>
</form>
</body>
</html>