Yes, ugly sites can make more in the short term, but a well designed site has much more potential than an ugly one. Poorly designed sites do often convert better when using adsense ads, but a ugly site is never going to grow to the size that a well designed site will. I use to own BusinessIntelligenceAnalyst.com and it was an ugly site that converted great with adsense and made at its peak around $10 a day. (Site built with Prosense Blue WordPress theme)
People argue that with ugly site visitors are going to click on the first things they see to get off the page, which most of the time are ads. The content is often thin and not helpful to users so they look for other links to help them find what they came looking for. Visitors do not enjoy visiting ugly sites.
The problem with a site like that is the potential is limited. My site was never going to become an authority site on the topic with that theme like that. Visitors are not going to share and comment on a site that does not build trust. With a well designed site you may not have a 10% CTR, but you are going to attract more visitors, links and advertisers. Other webmasters are going to link out to a better looking site, not some made for adsense wordpress theme. If your site does grow larger, you also have a better ability to attract direct advertisers with a well designed site. Overall, you are giving yourself credibility by using quality web design.
You do not have to have a perfect design, or spend thousands on design to have a nice site. Just pick a simple design and do not crowd it with ads above the fold. If you are find creating a small minisite, which I advise against because ranking them is getting harder and harder, you may do better in the short term with an ugly theme. When you want to become an authority site in your area make sure you have a design that customers will trust as an authority site. A great site does not have to be perfect, it just needs to appear professional so that the readers trust it.
Do you own ugly or great looking sites? I own a bit of both, but am moving towards building authority sites.