I think this is mostly a matter of the situation.
Consider pathnames. The standard prelude has "type FilePath = String" because, as a matter of convenience, you want to have access to all the string and list operations. If you had "newtype FilePath = FilePath String" then you would need filePathLength, filePathMap and so on, or else you would forever be using conversion functions.
On the other hand, consider SQL queries. SQL injection is a common security hole, so it makes sense to have something like
newtype Query = Query String
and then add extra functions that will convert a string into a query (or query fragment) by escaping quote characters, or fill in blanks in a template in the same way. That way you can't accidentally convert a user parameter into a query without going through the quote escaping function.
