I can tell you from experience...transfer to/from the airport in Venice and to/from the Rome Fiumicino Airport is super easy. I think it costs us about 11 euros per person (in 2007) for the Alilaguna Boat in Venice and 10 euros per person to take the train from the Rome Termini station to the airport--and children under 12 were FREE (we walked to the Termini from our hotel, but pretty much ALL bus stops had a bus going to the Termini it seemed). The Venice airport is small and the boat transfer drops you off at the pier and you follow the signs lugging your baggage. It is about a 10 minute walk along the sidewalk from the pier to the terminal doors, but it is very easy to see what you are supposed to do. There are several pickup points throughout the Venice waterfront...your hotel can help you arrange it and will tell you which to go to. The WORST part is pulling your luggage along the bumpy stone streets of Venice...the less luggage you have, the better!!! Sooo...I say if you can save HUNDREDS by booking your pre- and post- stay hotel yourself, depending on how many are in your party needing a transfer, you are going to save quite a bit by booking yourself and paying for your own transfers. It would be worth it to me. But if you will save less than $100 dollars on each end to book on your own v. ABD, it might be worth the extra $50-$100 bucks on each end to just let ABD do all the worrying for you.
In Venice, we stayed at a lovely hotel called the Concordia Hotel right on St. Mark's Square (it was so close that I could actually see INSIDE St. Mark's basilica from the balcony of the room). I paid 110 Euros per night, booking it on hotels.com. I took a quick peek at their website and saw that their listed rate is 330 euros this summer, but who knows, you might could surf the travel sites like I did and stumble onto a gem of a hotel like I did for a great price. I don't remember the name of our hotel in Rome, but I do remember I paid 90 euros per night. I found it in Rick Steve's Rome book--clean and great location. Again these are all 2007 prices, but I think euros were costing about $1.37 US then.
Try this website for info about getting to/from Rome's airport:
www.goeurope.about.com/od/rome/qt/rome_transport.htm.
Also, I believe I remember that it was about a 40 euro cab ride to or from the airport into Rome.
I really think you can do it on your own with little hassle in these two city's airports, and I am flabbergasted at those prices---egad!!