Check source contain replace string
Method names should be named using PascalCase casing.  
An if condition is just a boolean expression hence if (!string.IsNullOrEmpty(source) == true) is a little bit over the top. Either write  

if (!string.IsNullOrEmpty(source))
{

}


or   

if (string.IsNullOrEmpty(source)) { return source; }  


which saves one level of indentation.  
Why is the method protected ? Doesn't make sense to me.
The name of that method sounds rather like a class/object name than a method name. Methodnames should contain a verb or verb-phrase.


Instead of the Regex stuff and string.Contains() etc your method could just look like so  

private static string SuperscriptRule(string source)
{
    if (string.IsNullOrEmpty(source)) { return source; }

    return source.Replace("&lt;sup&gt;", "^").Replace("&lt;\sup&gt;", string.Empty);
}