There is nothing wrong with saying "I'm sorry, but <fill in issue here>". As shog9 noted there is even a place for this faux-empathy in the pre-programmed error messages for some situations.
You will note that I use the wording myself quite often, although I often take it back a step. Instead of saying I'm sorry for my close vote (or whatever) I'll say I'm sorry the user is having a rough go of their first question (or whatever the case is). That's something I'm actually sorry about. Behind that I include a description of whatever the issue was. Some issues are fixable and include a call to action, others just are not and the education is just so they do not make the same mistake next time.
In short, there is nothing wrong with saying kind things.
The real issue here is that we also need to say true things. This subject was raised with you, not because of the language of apology or nice tone, but because of the content of what you were apologizing for.
someone needs to apologize for the random closures might as well be me -- caseyr547
We know you don't like or agree with the practice of closing questions or our site specific scoping guidelines. Before this issue of comments came up, you had disagreed with quite a number of other closures. In response we asked you to take your concerns to meta. Rather than duking it out in comments and confusing newcomers to the site, we wanted you to take any objections to the way things were being handled to meta where our community could consider your concerns. Rather than doing that, you started "apologizing" for closures that you disagreed with.
My response to you was along those lines:
No, no-one is going to apologize for "random" closures because they are not random. We even go so far as to comment on every single one explaining exactly what the issues are. If you disagree with the issues the venue to discuss that is meta, NOT comments on new users posts. -- Caleb
Anybody is welcome to follow the transcript to see how we ended up here. My concern now is that this appeal to SO meta is over the wrong issue.
The issue that needs to be taken to meta is your objections to our question scoping guidelines and usage of the closure system. There is no law against apologizing or being nice, but our guidelines on questions haven't changed. If they do, the place that will happen is our site meta, not comments on new questions.