I use iweb for my site (see sig) as I am a complete novice and do not know anything about coding at all. I have found it to be really good as far as being an easy way to customise things and create a web page to look exactly how i want it. I also host it on my mobile me account so i don't have to eve think about how to host it etc.
However there are the following things that i find problematic.
The site loads slightly slower than other websites, this i believe is down to the way it is coded or maybe the mobile me hosting.
It is not very search engine friendly. Searches for specific things i have written about are not very favourable to my post in the listings.
I haven't found an easy way or in fact any way at all to create any moving parts other than adverts and other flash type things such as youtube that you embed from other sites.
I have 2 podcast series which i host on my site and there is no way to see how many people are listening... (which is particularly annoying as one of them even got into the uk itunes top100 at one point... boast over!)
I am sure that there are a few other minor things, but all in all I am really pleased with what can be done with it, after all it is bundled software. The fact that it is so easy to use makes up for the downside, but if apple released a version that addressed the above issues then it would be becoming more like the perfect app... for me and my lack of coding knowledge at least!