Yes, in time non-ADA compliant websites will be penalized in the search engines. It's already on their radar. But for now they are still negatively affected, just in an indirect way. Live traffic behavior (user experience) is now factored into Google's algorithm and is a ranking signal. Negative user interactions absolutely have negative affects on rankings.
As organizations around the world scramble to bring their sites into compliance with the World Wide Web Consortium’s Web Content Accessibility Guidelines (WCAG), focus on other, preexisting accessibility regulations has also intensified. The United States’ Americans with Disabilities Act (ADA) is one of the most visible and complicated pieces of accessibility legislation. Let’s look at some of the ins and outs of what an ADA compliant website means today. Or, if you're interested in seeing the nitty-gritty details of your site's accessibility, request a free website audit report using the form on this page.
I own a medical practice in California with 5 employees. Since I have under 15 employees am I exempt from needing to have my website comply with the ADA? I know that my physical practice is exempt from ADA policies regarding employment (under 15) but I don’t know if that extends to websites. My website is not an important part of my practice and I don’t really want to sink any funds into it if I don’t need to.
We recommend following the Web Content Accessibility Guidelines (WCAG) as best practice on your site, which is what our platform uses as the foundation for our accessibility guidelines. To see how accessible your site is according to WCAG, request a website audit using the form on this page. Your PDF report will be emailed to you within one business day, so you can start assessing the conformance of your site quickly. 
Courts have essentially taken three positions when approached with this issue. Some courts take the position that the ADA applies to all commercial sites because the law was meant to protect disabled individuals from having a more difficult time than able-bodied individuals from doing business. That is why the website Scribd was unable to get a case summarily dismissed and ended up settling.