I haven't read too many modules, but the few that I have (mostly Shadowrun adventures from 2nd Edition) included flow charts, which to my mind were relatively well put together. I think the main issue with flow charts is, as has been mentioned, maintaining the balance between preparation and railroading. Depending on the set up, some railroading may be necessary (if it has a significant investigative component for example, requiring certain individuals etc to be contacted in order for the necessary information to be acquired), but ultimately I'm not a fan. I much prefer to sort of map out where clues or such (if it is such a situation, which in SR is fairly common) are and play it from there. If the players don't catch everything, they don't catch everything and the outcome of the adventure will not be too negatively impacted.
Ultimately, I think it depends on the GM and the players, you have to find what works for you.