What to reply to your former supervisor that wrote that your paper "isn't worth much" before submission to a journal? I am a recent Ph.D. graduate in computer science.
In the last few months, I wrote a paper about an aspect of my thesis, with the collaboration of my former supervisor. We found a call for papers for a "special section" of an important journal, that is a section focused on the data set we are exploiting. The submission deadline was set to the end of November 2014, but surprisingly we just discovered that it has been post-poned to the end of March 2015, a four month delay.
I did not know if it was better to send this paper to this "special section" or to the "normal track" of the journal, so I asked here on Academia.

User Geoff Hutchison suggested to me to contact the editorial board and ask them if I could have all the original time schedules. That means to have all the notification and re-submission dates as they were not post-poned, except the final publication date.
It seemed reasonable to me, so I wrote to my former supervisor (who is also the co-author of the paper, even if his contribution to the project and the paper is only around ~5%).

He replied to me in a very ill-mannered, thwarted and angry way, stating that "writing this request to the editors may cause a lot of problems", that I am "not able to understand how lucky we are for the existence of this special section", "having the paper accepted in this special section may be the best thing that could ever happen to our our paper", that I "should focus on how to improve the paper, instead of inventing new ways to create problems", and I should "understand that the paper isn't worth much".

What to reply back to this "gentleman"?

The paper is mine, comes from the doctoral thesis of mine, from an idea that I had, and was written entirely by me. My former supervisor just reviewed and corrected it.
I am not going tolerate this disrespectful behavior, and cannot stand having a co-author that considers my paper "not worth much".

[EDIT]: Thanks to all for your contributions. I'm asking to you all some suggestions on how to manage this situation: should I trust someone that is the co-author of my paper and thinks that the paper "isn't worth much"? In my opinion, this statement is in contrast with actually being a co-author of the paper.
How to let him know that I did not like his ill-mannered way to reply back to me, without damaging my perspective paper submission?
In the last months, I wrote a paper about an aspect of my thesis, with
  the collaboration of my former supervisor.


That means that the paper is not 100% yours. Do not add or remove co-authors on the basis if you like them or hate their guts. 


  Having the paper accepted in this special section may be the best
  thing that could ever happen to our our paper


Sounds like excellent advice. Special issues are more focused, have shorter response rates and usually easier acceptance for more focused papers.


  Writing this request to the editors may cause a lot of problems"


Also excellent advice. You want to contact the editors to do the review of your paper sooner just for you? This is simply stupid.


  should focus on how to improve the paper, instead of inventing new
  ways to create problems


You have four months to improve the paper. Are you sure that it cannot be improved? Are you afraid that your competitors might publish sooner? If yes, submitting to the journal now, will not save you anyway. Could you not upload on arxiv? You should also discuss this with your advisor. 

Conclusively, cool down. As a PHD graduate and not a student anymore, you must behave always as a professional. Perhaps your paper is not that great (perhaps it is). That is not an insult - it is the sincere scientific opinion of one of your more senior peers (who contributed to your success). Do not burn bridges with your supervisor, just because he expressed his honest opinion (even if you do not agree with that).