The Doctor's TARDIS has probably always had a force field generator.
As far back as the 3rd Doctor there was mention of the force field. In The Three Doctors, the 3rd Doctor's exile to Earth is lifted as thanks for his help against Omega, and he explains that he will stay on Earth, so that he can repair it. It's mentioned again at times, for example, in the 5th Doctor's Four to Doomsday, where it protects the Doctor from outer space when the TARDIS door is open.
At some point between then and the 9th Doctor, the force field apparently ceases to work (the Doctor's TARDIS has never been in good shape). In The Parting of the Ways, Captain Jack Harkness used a tribophysical waveform macrokinetic extrapolator to create a force field around the TARDIS, and we see this integrated into the TARDIS console itself.
Although the force-field can protect the TARDIS against many threats, we do see that
the Dalek Crucible in Journey's End is capable of destroying the TARDIS, although it has been disabled, so perhaps the force-field was simply not in effect.
Out-of-universe, I expect that Captain Jack's comment was a hedge by the writers so that they were justified in having something threaten the TARDIS in later episodes.
When the 10th Doctor regenerates into the 11th,
the violence of the regeneration causes significant damage to the TARDIS interior. When we see it repaired/remodelled, the extrapolator is no longer visible. However, we do see force-field effects with the 11th Doctor's TARDIS, so either the extrapolator is merely no longer visible, or perhaps the original force-field generator was repaired along with the rest of the TARDIS.