Looking at Guidestar.org, I see that for the 2006 season, NSMT had $10,446,776 in program revenue and $1,787,948 in donations (i.e., donations = 17% of sales)
The same season, Huntington Theater had $5,643,141 in donations and $6,454,327 in sales (donations = 87% of sales).
The same season, American Repertory Theater had $2,313,985 in donations and $6,008,847 in sales (38.5% of sales).
The same season, the Boston Ballet had $7,275,809 in donations and $13,975,242 in sales (donations = 52% of sales).
Analyzing those figures, it would appear that NSMT's fundraising performance was the real issue. Considering the size of the deficits, relative to sales, even a small increase in fundraising effectiveness - to, say, 20% of sales - would have put NSMT well into the black...
I haven't look at the information to verify these numbers, though.