It allows you to run your own DNS servers. Let's say you are hosting web sites for your customers, and in order to be able to register domains you are a reseller of a domain registrar. Most of these domain registrars offer something like "Managed DNS" which costs a little bit and uses the registrar's name servers.
Now whenever you register a new domain, you must specify name servers that should be responsible for the domain, so you can either buy "Managed DNS", or you specify your own DNS servers which saves you the money for "Managed DNS" (if you have hundreds of domains this can sum up...) and makes you independent because it's you who controls your name servers (imagine your registrar has problems with his DNS servers, or something in the "Managed DNS" web interface doesn't work, or you're allowed to make only 50 DNS changes per day but you want to move a server and have to update 200 domains at once or...)
With ISPConfig you can create DNS records, and whenever you register a new domain you can then specify your ISPConfig servers as authoritative name servers.
If you have two ISPConfig servers you can create the primary DNS records ("Master Records" in ISPConfig talk) on the first server, and on the second server you create secondary DNS records ("Slave Records") so that DNS is still available if one of these two servers fails.