You can use the Backup-SPSite cmdlet built into SharePoint 2010 and SharePoint 2013, which will only target an individual site collection. In the scenario you're describing, each of those site collections would need to have separate calls of Backup-SPSite in order for them each to be backed up. If you run the command below, it will only target the top-level site collection, which is what you're looking for:
Backup-SPSite -path http://www.site.com
If you were to want to do site collection backups for each of the site collections, you'd either need to populate an array of the site collections in the web application, or to name them each individually in calls to Backup-SPSite. By default the Backup-SPSite cmdlet will not iterate through each of the site collections beneath the root site colleciton if you pass it the URL for the root site collection.
NOTE: if you're using SharePoint 2007, you'll want to use the Backup operation for STSADM with the -URL parameter populated with the URL of the target site collection.
John