For Example: (remove div tag then the result is correct)
<zk:zk xmlns="native" xmlns:x="xhtml" xmlns:zul="zul" xmlns:sh="shadow" xmlns:zk="zk">
<x:html sclass="no-js" lang="en">
<x:head>
</x:head>
<x:body>
<div>
<zul:popup id="pop">
You should be able to see this after click button.
</zul:popup>
<zul:button label="please click me" popup="pop"/>
</div>
</x:body>
</x:html>
</zk:zk>