Your argument might be stronger if it didn't rely on labeling ...
The argument doesn't rely on labeling, though it does call a spade a spade.
A definition of "apologism" is "a defense or excuse, a speech or written answer made in justification." I'd love to hear why this is an incorrect characterization of the comment.
The short answer to your question is that you should concern yourself (not sympathize) with their problems when those problems intersect with yours and guide their decisions.
If I retain Matasano for work, I shouldn't need to obsess over the details of your cost structure or employee benefits packages; our contract should suffice. Similarly here, Patrick's description of Paypal's theory of underwriting is interesting, but irrelevant. Deflecting blame based on these issues is, indeed, absurd.
If PayPal's risk profile does not support doing business with Indiegogo projects, they should cease doing business with those projects rather than seizing thousands of dollars on spurious grounds. Feel free to debate the merits, if you actually have a difference in opinion.