The thing people tend to overlook is the fact that CS professors do not always have experience in the areas needed to design good interfaces. Making something work well and making a good user interface are often completely different skills; a web programmer is not a web designer, and vice versa. In most cases, you need to take specific design courses in order to understand what it takes to design a good user interface.
Ultimately, web design takes too much dedication of time for most busy people to consider investing their own resources even if they can build the website from scratch, and being able to build a website takes enough dedication already. It is also worth mentioning that being a professor of programming does not imply they know about web programming. For example, teaching data structures has no dependency on being able to use a database within the core of a website.
That being said, a "bad" design to most might have been the "best" design to some people. This is called an opinion, and these have changed a lot since just the past two decades. Just be happy tiled animated gifs and auto-play midi files have lost popularity since then.
And as for your site being too flashy, it depends on the situation and your personal preference. If you want it to be flashy, then go for it. However, the content of a personal site will have a bigger impact on more pragmatic people, which is common in the CS department. The most important aspect for a personal website is to provide a quality experience for the right situation in order to show you know your stuff. This will vary depending on what you need to accomplish.