I book with a TA to have that little bit extra piece of mind... someone to "have my back" as it were if things go sideways.
We did Peru and the Amazon with Avalon a few years ago. Our flight leaving Toronto was quite late - and we missed our connection in Miami. (Actually, the plane was still at the gate - but the gate was closed.... so close...). Anyway, by the time we made it to our hotel (air line arranged and paid for) it was almost 4 am. We had another flight booked from Lima to Arequipa - for noon. Obviously we weren't going to make that.
A quick e-mail to our TA at 4 am told her about the issue - and asked if she could change our booking to the first flight the following morning. She phoned me before 10 am - the flight had been changed, and the change fees charged to the credit card we had on file. When we returned home, she had all the paper work waiting for us to claim the change fees, and the one night in the hotel that we missed.
I always do my own research for river cruising - but always use our amazing TA for the booking. Even if she charged for her services (which she does not...) she would be worth it.
Fran