Why had he flown Tru out so far in advance?
As the breeze picked up, the moon began its slow ascent into an indigo sky. He took it
as a cue to head back. He assumed his father owned the place. It might have been a
rental, but the furnishings were too pricey to trust to strangers, and besides, if that was
the case, why not simply put Tru up at a hotel? He wondered again about the delay until
Saturday. Why had he flown Tru out so far in advance? If the man was indeed dying, Tru
speculated that it could be something medical, which meant there was no guarantee
about Saturday, either.
What does "Why had he flown Tru out so far in advance?" mean?

Question

Why had he flown Tru out so far in advance?
As the breeze picked up, the moon began its slow ascent into an indigo sky. He took it
as a cue to head back. He assumed his father owned the place. It might have been a
rental, but the furnishings were too pricey to trust to strangers, and besides, if that was
the case, why not simply put Tru up at a hotel? He wondered again about the delay until
Saturday. Why had he flown Tru out so far in advance? If the man was indeed dying, Tru
speculated that it could be something medical, which meant there was no guarantee
about Saturday, either. 
What does "Why had he flown Tru out so far in advance?" mean?

Answer

Peter and Steev's answers are both good.  Just to clarify:

To "fly someone out" is to pay for someone else to take a flight, or to arrange for someone else to take a flight

The phrase "so far in advance" means "so early" ("so far" = very far; "in advance" = before the necessary time).  It implies that there is some event that will happen at a particular time, but you are prepared for before that time.

So Tru is wondering why the man paid/arranged for Tru to take a flight at such an early time.

Answer

I guess "he" had paid for Tru to be taken by air to somewhere . ", So far in advance," would mean that it was much earlier than was needed which is puzzling him.

Answer

Why did he come and visit (take a flight) would be the literal meaning.