Whether or not you should respond to their e-mail depends on how you
want to be involved with the current meeting and the community
supporting the conference.
Acknowledgement of a rejection e-mail from conference organizers is
generally not necessary unless they have requested confirmation or
You mentioned an interested in "keeping up to date" with this conference, presumably with the intention of presenting here in the future. However, it may still be possible to participate in the current meeting if you make an effort to politely contact the organizers as soon as possible.
Every conference is a little different, since they are organized according to the preferences and constraints of the core group of researchers that plan and organize the meeting. Often there are poster sessions or other opportunities to present your work in lieu of a presentation if it is suitable for the conference.
Before you decide to contact the organizers, you should carefully re-read the original call and conference description. Since your paper was not selected for presentation at the conference, there may be a problem with: (1) the perceived quality of your submitted manuscript, (2) the format of your submitted work, or (3) the topic that your paper addressed.
Check the call and double-check your submission to make sure there are no obvious discrepancies that would disqualify your work. Make sure your paper is on-topic, in the correct format, and of suitable length.
If you are new to a subject area, or a particular conference, your impression of what it is all about may not match up with the actual meeting as well as you might expect. It may be that your submission was off target for this conference and could be amended with a little communication.