Agreed. Users care more about getting the task done then having an emotional relationship with the system. To inject sympathy into what need only be informative/instructive, is to call attention to the user's ignorance in fabricating false expectations of the system. That's more offensive than anything else.

Only in the case of the system inadvertently failing to meet the expectations it made (e.g. database server inaccessible) would apologetic messaging be considered.