Sometimes, The Doctor is forced to hide certain truths from his companions to protect them from harm. There is a big, bad universe out there after all, full of many dark and dangerous monsters that want to have them for supper. Occasionally, the less one knows, the better for everyone. If only that was always the cause of the Doctor's lies.
Whether a relatively young Time Lord meeting their greatest foe for the first time, entirely due to the Doctor's stubbornness, or an older being full of regret, false memories, and fancy dreams to help them sleep at night, the many lives of the universe's most famous traveler have been intertwined with deception, all the way along.
It would be too kind to say that they lie to keep everyone safe. It would be too harsh to say that they are devious in their deceptions as well. Rather, perhaps it is best to follow River Song's advice and to remember rule number 1 of traveling with The Doctor: The Doctor Lies. So anyone hoping to travel with them had better get used to that very quickly.
10. The Timelords Were The Good Guys
The Ninth and Tenth Doctors were the freshest faces who had to deal with the Time War, the loss of Gallifrey and the destruction of the Time Lords. They both chose to deal with this in different ways. For the Ninth Doctor, he was more likely to keep silent on the whole affair. He told Rose that he was the last of his kind, though that would be one of the last times he mentioned it.
The Tenth Doctor, while not exactly starting conversations with it, was a little freer in speaking about it. He told Martha about Gallifrey, describing it as a beautiful paradise. He would go on to describe it to Wilf as well, telling the man about his people, how good and just they were, all while seeming to long for any way home.
However, this turns out to be a romanticized version of the truth. When the Master successfully opens a portal for Gallifrey to break the time lock and return, the Tenth Doctor is terrified. His fantasy is shattered, knowing that the planet had descended into Hell by the last day of the Time War. The Time Lords themselves had broken all of their sacred rules, throwing everything they had against the Dalek fleet.
The Doctor may once have been correct about his people and their ways, though the race that tried to escape the war was a far cry from this dream.