A lot of it comes from 1) inexperience and 2) bad frame design. How many people have you seen swear off of an entire company because of a singular bad experience with a single product? Those people are called idiots.

I have a Domane and a Crockett which both have internal cables. The Domane came to me completely unbuilt, so threading cables for the first run was definitely not what I would call fun, but it wasn't the end of the world. Having worked on many bikes in the shop with internal cable routing, I had a few tricks and it was all okay. The Crockett came as a frame, but Trek was nice enough to run some sheathing through the frame to ease the build process. That was much appreciated. The worst time I ever had working on a frame with internal cables was a Scott. But that was also the FIRST time I had done it, so I did a lot of stupid things. I didn't do those stupid things after that.

Sometimes the frame design is awful. The new Madone is awesome, but as someone said, you probably REALLY don't want to run mechanical on it. It's extremely specific. There is a chart for what cable length to run based on how many spacers you are running, because there is zero room for excess slack like you would have on any other frame, because it's FULLY internal. I mean, they give you the length down to the mm. Too long and you're going to have a hard time clamping everything down. Too short and you're not going to meet the stops and shifting and/or braking just won't work. You might be able to get away with removing maybe one spacer without having to recable it, but I haven't worked on one of those, so I couldn't tell you for sure. Woe be to the shop that has a customer who insists on reducing his stem height one spacer at a time on his Madone.

Also, as some have mentioned, some frames make noise. Definitely not all. But some will say "internal routing is noisy" regardless of frame. Those people are called idiots.

And I went a few rounds a couple of months ago with some people on this board regarding the cleanliness of internal cables. In my opinion (and in my general experience), internally routed cables are much less prone to corrosion. External cables tend to take in moisture and dirt into the housing at the exposed stop points. On some bikes, you can pull the cable out of the stop, move the housing, and clean and lube these points (but you still can't clean inside of the housing), but on any shifters with cables routed under the bars, you're not going to be able to pull those back to clean/lube the cable unless you're also doing bar wrap. With internal cables, you're much, much less likely to get moisture and dirt into the cables. Exceptions are provided for particularly bad designs. The one mentioned in that thread was the Specialized Transition, a tri bike, that had this collection of stops JUST below your chin in an aero position where you could just drip sweat all day directly into your cluster of cables. Great idea, Specialized.

Oh, that reminds me: working on ANY tri bike sucks, so those don't count when talking about internal cables.