I’ve booked (and been on trips booked by others) electronically, and almost never had any problems related to the electronic booking. Let me think of the worst things I can think of that have happened to me . . .
One thing that’s happened maybe twice, was the hotel charging a slightly higher rate than was agreed online. The only time I remember for sure that happening was with a hotel in Italy, and it was a long long time ago. I think they may have (intentionally or just by mistake) checked us in as if we’d just walked in, ignoring the reservation with the agreed rate. It didn’t make a huge difference in the price, and I think that’s an Italian issue rather than an electronic issue (I’ve seen a similar thing happen with an Italian taxi ride, and another crazy Italian hotel scam that didn’t involve electronic booking), but the way to head it off is to confirm the rate when you check in.
Oh, another thing that can be evil, is rental car companies. I had a reservation for a rental car at a certain rate pre-arranged electronically, to pick up in Dublin airport. When I arrived, they wouldn’t honor the rate, and wanted to charge me much more. However I stepped to the next door rental car agency (or maybe I had to try two) and was able to just book a car on the spot for much less. Again, that’s not necessarily about the electronic booking aspect – they might do that too if I’d made a reservation by phone.
I’ve had good luck with AirBnB, but I’ve heard tales from friends about some weird and problematic experiences there.
Checking details is important, and you’re often on your own to make sure things like whether you’re getting a smoking room or not, bed types, cancellation policies, etc.
The main thing I dislike about online trip planning is how much time it can take me to do it, seeing which site has the best price, what’s available on what date for what price, etc. There are still travel agents who can handle all that, but of course they have their fees.
Overall, I would say there isn’t much to fear from electronic booking itself, unless you get confused by the process and/or miss some details (fairly easy to do, especially if you’re new to it, but happens to me too sometimes because it can be brain-numbing using those web programs).
Of course, you can also still just use the Internet to find places, and then phone them up. Haggling for lower prices (if you want to do that) may still be easiest by voice.