To answer your question you need consider the following:
1. Ease of use can be more important that exquisite design - Average person does not value design as much as other things such as ease of use.
$0 site that is easy to build/update and done in hours/days > $$$ for beautifully designed by some flaky web designer/developer that takes 4 months to go live
2. Weebly's Design isn't that bad considering how flexible and forgiving the product has to be.
3. Please show me an example of a comparable product to Weebly that is as easy to use and get live but is significantly better designed?
If such a product exists then the answer might be marketing. Rob Walling of Startups for the Rest of Us Market > Marketing > Design > Product (functionality)
It's sad as a developer to see that Design and Functionality come after market/marketing. It also seems to contradict a bit of my point about ease of use for non techies being a reason for Weebly's success, but if they market well, and it's free then they have a huge leg up.
Really considering what it is Weebly aint too shabby. It's also amazing how many crappy sites there are out there that people continue to utilize. I did some cold calls for my startup idea and I thought the people with crappy sites would certainly get on board, but it didn't quite work out that way.