If you have to use Flash, then that's fine. But the author of the article is right IMO. You need to provide a compelling reason for me to hop off my iPad and boot up my workstation/laptop to look at your website.
I have long considered that Unobtrusive Javascript to be one of the best paradigms for websites. It shouldn't be that hard to do. In fact, even in web applications there should be a clear seperation of content and behaviour, just as there is to seperate content and style. I was looking at a VMware product the other day that does ITSM, and it was the most god-awful mix of bad Javascript and HTML that I was most surprised. Not only did it not use Javascript in a sensible way (ala jquery, YUI, etc.), but it used stupid tricks like document.all - and in fact the webpages that it loaded entirely relied on Javascript working.
Therefore, I submit to you that by not designing your websites with Unobtrusive Javascript, that you are a. causing accessibility issues (and NOT just for disabled users), and b. you probably haven't developed your website very well anyway.
Please, I urge you to convince your users WHY they need to turn on Javascript to use your site. If you can't provide a compelling case, then I'd suggest that you probably don't have a good reason to require it!