While I've never booked on line, I won't hesitate to do so the next time we cruise. This last time I was booked thru our local AAA and ended up transferring my booking to an agent out of Ohio because her prices were so much better (I think cruisecritic.com is a great website to get info....that's where I found out about this agent).
I think it's the fear of not having a person in front of you to do business with. These online agencies, due to their volume, can offer better prices and more shipboard credit. If you're not comfortable speaking to an agent over the phone (you don't have to do it all over the computer, you can call these online agencies), then you may need a local travel agent.
I've priced cruises from quite a few online agencies and if the price was right, I would not hesitate to book. This next time will also be my 5th cruise so I'm starting to feel comfortable doing everything on my own.
The above poster is correct about booking your own airfare and excursions. When we were in Alaska, we booked everything independently. I booked through the cruise line when we were in Panama this Christmas though.....I wanted to make sure I didn't get left behind in a foreign country! I'm not that comfortable doing everything myself yet!