Cobertura is an inactive project. Check out JaCoCo as a viable replacement, and it supports aggregate.
But if the issue is related to the NPE you get, check out this: https://jira.codehaus.org/browse/MCOBERTURA-151. We're using 2.5.1 of that plugin w/ that patch applied and it allows us to build using aggregate, but the output isn't really aggregate.