Company valuation only depends on future cash flows. If an asset is able to produce future cash flows, or can be sold to create cash flows, then this can be accounted for in valuation. In this article their mention of assets is actually assets under management (Link at end of comment). Assets under management still only factor in valuation based on their ability to generate future cash flows, as E-Trade have no claim to those assets. These cash flows have been taken into account, and then used to evaluate a $13 billion price tag. Elsewhere in the thread you can see how money is made from assets under management.
