Thank you so much for the feedback! Funny thing is, the publisher called me the day after I posted this. He is always very apologetic and a nice guy, but I told him I would need prepayment going forward, which he said he can do for web articles, and pay 50% up front for print articles. They get the majority of their money from advertising, so I understand that part.
However, I also talked to the web editor I've worked with (who I love), and they still owe her $900. I think that's really crappy. The publisher kind of threw her under the bus saying, "I didn't know the volume of articles J was having people write and publish, that's why we got behind." I ain't buying it, and it's become more of an ethical conundrum because it's just not right to not pay someone for the work they've done. The paltry amount they were paying her for the amount of work she was doing is outrageous. Meanwhile the print editor is kind of a jerk and doesn't seem to do much.
I know I shouldn't consider other people part of the equation, but if he treats someone who has worked for him for five years this way, I feel like I don't even want to be associated with him. There is a positive side: I enjoy the work, and it's good for building my local business. I'm still confused!