A number of annoyances I find in web design appears to stem from a desire to mimick print media such as newspapers. It is probably unintended and unconscious for the most part, but nevertheless it has annoyned the hell out of me too many times, so I've decided to write up all of my arguments in one place.
My most common and obvious web annoyance is black text on white background. It has an obvious lineage with print media, but there are a number of reasons why it fails on most computer screens.
On many print media, it's only possible to print darker ink on lighter background. There is no such limitation on computer displays. You are free to choose other colors based factors such as ergonomics. A discussion on this topic considers the pros and cons of various color schemes, noting for example that green-on-black is quite ergonomic, but little used today as it looks outdated like text terminals.
A white paper is a neutral background, whereas white on a computer screen (CRT or LCD) is a light source. If most of the screen is white, reading is comparable to staring at a lightbulb.
Some people have commented that I should turn down the screen contrast/brightness in case it feels like a lightbulb. The problem is that in many cases you need that contrast, but prolonged reading is not one of those cases. In other words, I want to have extreme black and extreme white available on my system, but it's irritating to the eyes to experience them all the time. HOW ABOUT I START SHOUTING AND ASK YOU TO TURN DOWN VOLUME AT YOUR END?
HTML describes the logical content of web pages, for example denoting which part of the text is a heading. It's ultimately up to the viewer to decide what a heading looks like, though HTML and CSS can give lots of hints as to how exactly present the content.
One reason behind this design of HTML is that people can view the same content on a variety of devices, for example cellphones. An exact graphical design is usually bound to a definite size and shape, for example A4, which is hard to read on small portable devices. On the other hand, plain text with logical markup is easily adapted to a range of sizes and shapes.
More generally, the Web was designed for information dispersal, and people have their own preferences as to how exactly work with the information. It's flexibility that liberates from some of the technical constraints of printed books. In cases where graphical precision is required, there are many good alternatives such as Postscript and PDF.
Ever wondered why newspaper text is laid out in relatively narrow columns? It's much easier to read that way, due to the limited range of eye movement.
Of course, columns on websites are a bad idea, because you'd have to scroll up and down repeatedly to read something. On the other hand, a web page is not limited in height, so the text can form just one relatively narrow column.
This is largely a presentation issue, so bad design can be mitigated by the viewer. For example, many web pages define the width of the text column in relation to the browser window. So for easier reading of most web pages, don't maximise your browser to fullscreen size.