I actually did sort of like them. I just wish there was more to do. Honestly, the first game had much more potential to explore, but they kept us confined to just one room (okay, fine, two rooms, maybe even three, but all were boring) when we could have done so much more. There was a bathroom with no purpose, since you couldn't go, and I would have loved it if Desmond was able to find a ventilation shaft or something in there to snoop around and dig up some of abstergo's secrets. But no, all you can do is sleep and check some guy's email.
Either way, it was a nice way to break up the somewhat repetitive gameplay in AC1, sort of like the breaks in MST3K where the viewers took a break from too many jokes (you win a cookie if you know what I'm talking about.)
I think Assassin's Creed 2 had a good balance between outside and inside the Animus though.