To be honest, my biggest Amazon Prime purchases are around the holidays or events like birthdays/weddings/baby showers etc. It is so much easier to just order something and have it shipped -- the sheer convenience of it all makes it worthwhile.
While I may order a 3-4 orders a month for most of the year, I end up ordering at least three times that during the holidays.
I try and make sure that my local bookstore gets my business -- but sometimes, I just don't have the time or the energy to look for a book, only to find that they don't have it yet. Especially when they're written by authors who aren't particularly mainstream. So, I can pre-order some of these books by my favorite authors, which is a huge perk.
There's also something to be said about impulsive shopping -- for instance, I just saw a book that looked quite interesting, and it was under $10. Normally, shipping would have been expensive relative to the cost of book, but given that I have Prime, I just ordered the book. A few weeks ago, it was a sandwich maker.
Prime Membership also provides you with "subscribe and save" offerings that I take advantage of (whey protein for my workouts, diapers etc).
So, yeah. Personally, I think that even at $99, it is definitely worth the money.