In an earlier article they noted:
That the project is already so far overbudget is a foreboding sign. Portland’s previous mayor, Charlie Hales, examined a similar homeless “navigation center” concept, only to conclude such a center would be prohibitively expensive.
So this was already an idea that was passed on because it would be too expensive.
In this one they also note that this project hasn't raised much money, and a large portion of what they do raise goes back out to cover travel and salary for one of the people who started/own the non-profit:
But on Harbor of Hope’s 2017 tax forms, the organization was nearly $110,000 in the red, due to a more than $100,000 loan that covered expenses while Williams and others raised little more than $8,000. The year before Harbor of Hope reported nearly $130,000 raised -- most of it gone by the end of the year due to travel, salary for Mazziotti and payments to contractors.
So it's a project that was already deemed too expensive that the city is now helping fund (more than they already have through giving them the land to use and waiving fees) because it's too expensive for the people who wanted to ram it through anyway (one of whom is now collecting a salary from it).
(Before someone chimes in to defend the salary thing: I understand the need for people running non-profits to get paid to some degree, but I think this is different given the specifics of this situation.)