I’ll expound later, but one grain of rice to drop in the cup – the TARDIS is as much a living being (sentient, opinionated, and at times, temperamental) as she is a vessel, but in nearly all instances where the craft appears to be self-navigating or reacting, it was explained that some setting/programming/adjustment was done beforehand. She does have an impact on the destination, and often the path, but that is often described as the influence of her free will on the actions already set in motion.
Specific systems were put in place to provide for self-navigation, remember. Aside from the recent revival of the HADS system (Cold War), we also had the emergency system that would reunite the TARDIS and Doctor if separated (Wedding of Sarah Jane, Blink). Of course, this seemed to require a little more manual involvement recently from Clara (Hide) to get to the Doctor, but that may have been the complexity of traveling into a pocket universe to retrieve him. Not your usual skip up the lane to the pub, there.
Lastly, and before I get fired for ignoring my PAID job, recall that the TARDIS could run into situations where it was adrift and unmanned (Voyage of the Damned), and needed a specific response system in those cases to lock on to the nearest major gravitational source. A few similar failsafes were described in EU novels, and a few 6th Doctor radio plays (the titles of which escape my memory at the moment, even though I’m looking at them in iTunes as we speak…er…type). Were she able to self-adjust and propel, these safeguards wouldn’t be necessary.
