For the v1 of multiple subscription support, we don't combine subscriptions into one charge. Hopefully we didn't get a biased sample, but we asked some of our beta users about their preference here and the consensus was for keeping each subscription separate -- per-subscription invoices, and thus per-subscription charges. At the very least, this is likely the simplest thing to reason about, in terms dunning and various unpaid / past due states.
I could definitely see us allowing lumping subscriptions into one charge, at least as a configuration option.
One thought is that the right solution might be to support specifying at creation time that a subscription's billing cycle should 'snap to' another's, leading them to be invoiced and billed jointly going forward. Would definitely be happy to discuss these use cases more -- jim@stripe