It is a risk for any firm to be highly dependent on one customer for most of its revenue and SETI appears to have been highly dependent on US government funding.
It is dangerous to make conclusions based on a newspaper article, but it seems they found $50 million in private donations way back when to build the network. Now they can't find $2.5 million per year to run it?
If nothing else, something is seriously wrong if donors that ponied up $50 million to build the Ferrari no longer want to shell out $2.5 million run it.
The quote: "if everybody contributed just 3 extra cents on their 1040 tax forms, we could find out if we have cosmic company." suggests that the organization is focused on government funding, rather than individual donors - and continues this focus even after an evident failure of that model to keep things running. Meeting the needs of government funders and meeting the needs of donors are entirely different things. In my experience, you can have one or the other, but not both.
They should step back and rethink how they can make their non-profit work primarily based on voluntary donations. The world is full of non-profits that manage it with budgets much larger than the $2.5 million/year SETI appears to need.
Link to send SETI money: http://www.seti.org/page.aspx?pid=1468