It actually isn't at all surprising. Every time there has been a new communications technology, it has taken a very long time to figure out how to best use it.
For example, page numbers did not appear in books until sixty-five years after Gutenberg developed the printing press. The earliest moving pictures didn't have close-ups, pans, or cuts.
Sometimes it just takes a while for the technology to mature to a point where you can do useful things. For example, it was hard to do zooms in early cinema because the focus changed as you zoomed. The first "parafocal" zoom--i.e. one that stayed in focus as you zoomed--didn't go on the market until 1946.
But it also takes time for people to try different things, to learn what works and what doesn't. This is hampered by memories of the old way of doing things. For example, in Gutenberg's time, lots of scholarly works were still written on scrolls--which have no pages to number. Even for codexes-- books with individual pages--page numbering wasn't an obvious concept because books were made one at a time. With different size handwriting and different size pages, what was on the 34th page of one copy might be completely different from what was on the 34th page of a different copy. And if you'd never seen a page number before, how would you know that they were useful?
Email is in the same awkward stage as early books. One symptom of email's immaturity is that different email programs have radically different features and capabilities. Oh, sure, the basics--reply, forward, delete--are the same, but once you get past the basics, the capabilities are very different. For example, Outlook Express has a Mailing List Manager, Outlook has amazingly flexible views, and Eudora lets you save searches. However, those features are only in those programs. If we all knew the best way to handle email, all email programs would have the same features.
I think that email programs suffer from an over-identification with filing cabinets. Email has this legacy of organizing by moving messages into different folders, like you file messages in a filing cabinet. However, filing cabinets don't have Search' boxes. You can't walk up to a filing cabinet and ask it to give you all the memos from your boss from the past month. With a filing cabinet, it was important to use a filing strategy that minimized retrieval time. With email, it's more important to use a strategy that minimizes filing time. I suspect users can usually get by with just two folders: the inbox for messages-in-progress and another folder for messages that users are done with.
And, because of the legacy of filing cabinets, people don't make good use of built-in tools (called filters or rules) to organize and prioritize messages. The canonical email management advice is to use filter to move messages into different folders as the messages arrive. But I found when interviewing email users that most didn't like that technique. They wanted to see all the messages that they had to deal with in one place, not spread across a bunch of different folders.
This makes sense: you don't put your postal mail into your filing cabinet before you read it--you organize it into different piles but leave it on your desk where you can see it. So really what you want is for your active messages to stay in your inbox, but in some sort of organized and prioritized list.
Unfortunately, email programs don't make that technique spectacularly easy to discover or implement. (With some, it's not even possible.) What you need to do is use your filters to change something about the message that you can sort by, then sort your inbox by that. For example, with Microsoft Outlook, use your filters to assign a message's Category, then set up a View that Groups messages by Categories.
The good news is that email programs clearly are going to get better. Spam filters are going to get a lot better, and it will be much easier to organize messages.