This is not average for Flash. Normally, the only cause for long export times is that you're exporting a lot of stuff, some of which you may not mean to be exporting.
Does your animation have audio? If you imported audio into your FLA, then that sound has to be encoded every time you export, and that takes a while. The best way to deal with this is, in publish settings, set your audio compression to "Raw". This will publish the audio uncompressed, so it will increase the file size but publish instantly. (Of course when you are ready to export the finished product, you'll want to return the settings to a compressed format for the final export.) Alternately, you can put the audio in a separate file (SWF, MP3, etc) and load it at runtime.
Another common mistake is to accidentally embed a large font. If you have dynamic text fields using embedded fonts, it's possible to embed an entire font, which for unicode fonts can take several minutes. It's easy to check if you're doing something like this - in publish settings, turn on "generate size report". Then export, and check the size report for any large pieces of content that you didn't mean to be exporting.
It's hard to say more without knowing what kind of content you're exporting, but if you have one piece of content that takes much longer to export than similar pieces of content, then the cause is probably something along these lines.