I don't know of any pre-existing solutions, but you can do this with netfilter using the 'owner' match extension, although you'll probably have to play with conntrack a bit to catch and account for the inbound packets (and you'd miss the initial connection setup packets, as they're not managed by a userspace process). I'd imagine that a non-netfilter solution would also be possible (a la ntop and the like) but it'd almost certainly get ugly and CPU intensive very quickly.
Honestly, though, I have pretty serious doubts that you're solving the right problem. Accounting for traffic on a per-user basis is better done by analysing the server-level logs (Apache, MTA, POP/IMAP server, etc) and accounting/billing on that basis (with an appropriate overhead for the bits they don't catch, like DNS). Trying to tie everything back to a user almost certainly won't have the results you expect.