Advertising paid for rent, wages, health insurance, utilities, all the normal stuff that you pay for when you have fourteen souls working together. That money keeps the lights on while we do the things people expect from us: thrice weekly content drops, two annual shows, the scholarships, Child's Play, etc.
The shows make money, otherwise they wouldn't do them. By most accounts they make a lot of money. PAX Prime 2011 had 70k attendees (according to Wikipedia) and at $65 a pop that's a hefty (~$4.5 million) in revenue not to mention what exhibitors pay (which can't be cheap for the target audience). They make more than enough money off of this to go ad free.
The scholarships are their problem, the comic reader gets nothing out of those except warm fuzzies.
Child's Play should be able to maintain itself on low overhead and a non-profit status. It should cost them a minimal amount of money and any it does the company can directly write off.
Asking the community for $1 million every single year to draw a comic seems a bit steep.
I'm not saying it's not worth it. I probably will contribute, but it feels like a lot of for a small thing.
I get the feeling that they want to change this perception, especially with the recent hire of Ben Kuchera to write full time news and commentary for the Penny Arcade Reports site.
Anyway, I think you're probably right.
Here's the important part though, they're already paying it, and more. That's how advertising works. People buy stuff that's advertised and they pay a higher markup which goes to pay for the advertising which goes to pay for the content.
The only difference is that today it's very indirect. What's wrong with direct support?