I have used the above article and added MasterPage and Content Page using MaterPage and its working. I am not sure where you are stuck.
HTML
<%@ Page Title="" Language="C#" MasterPageFile="~/Site.master" AutoEventWireup="true" CodeFile="Default.aspx.cs" Inherits="_Default" %>
<asp:Content ID="Content1" ContentPlaceHolderID="head" Runat="Server">
</asp:Content>
<asp:Content ID="Content2" ContentPlaceHolderID="ContentPlaceHolder1" Runat="Server">
<asp:ScriptManager ID="ScriptManager1" runat="server">
    </asp:ScriptManager>
    <asp:UpdatePanel ID="UpdatePanel1" runat="server">
        <ContentTemplate>
            <asp:TextBox ID="TextBox1" runat="server" TextMode="MultiLine"></asp:TextBox>
            <asp:HiddenField ID="HiddenField1" runat="server" />
            <br />
            <asp:Button ID="Button1" runat="server" Text="Submit" />
        </ContentTemplate>
    </asp:UpdatePanel>
    <script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
    <script type="text/javascript" src="jscripts/tiny_mce/jquery.tinymce.js"></script>
    <script type="text/javascript">
        $(function () {
            LoadTinyMCE();
        });
        var prm = Sys.WebForms.PageRequestManager.getInstance();
        prm.add_endRequest(function (sender, e) {
            LoadTinyMCE();
        });
        function LoadTinyMCE() {
            $('[id*=TextBox1]').tinymce({
                script_url: 'jscripts/tiny_mce/tiny_mce.js',
                theme: "advanced",
                plugins: "spellchecker,pagebreak,style,layer,table,save,advhr,advimage,advlink,emotions,iespell,inlinepopups,insertdatetime,preview,media,searchreplace,print,contextmenu,paste,directionality,fullscreen,noneditable,visualchars,nonbreaking,xhtmlxtras,template",
                theme_advanced_buttons1: "save,newdocument,|,bold,italic,underline,strikethrough,|,justifyleft,justifycenter,justifyright,justifyfull,styleselect,formatselect,fontselect,fontsizeselect,spellchecker",
                theme_advanced_buttons2: "",
                theme_advanced_buttons3: "",
                theme_advanced_buttons4: "",
                theme_advanced_toolbar_location: "top",
                theme_advanced_toolbar_align: "left",
                theme_advanced_statusbar_location: "bottom",
                theme_advanced_resizing: true,
                height: 200,
                skin: "o2k7",
                skin_variant: "silver",
                setup: function (ed) {
                    ed.onChange.add(function (ed, l) {
                        $('[id*=HiddenField1]').val(l.content);
                    });
                }
            });
        }
    </script>
</asp:Content>