This was addressed in the source novel; [Harry Potter and the Deathly Hallows][1]. The Ministry of Magic has been thoroughly infiltrated. Since Harry Potter still has the Ministry's [Trace][2] on him (basically a magical charm that detects if magic is being used around an underage wizard), if they attempt to apparate him (or if he attempts to apparate himself), Voldemort's Death Eaters will be informed of it and will be able to abduct him with ease.

> ‘We are at an advantage there, my Lord,’ said Yaxley, who seemed
> determined to receive some portion of approval. ‘We now have several
> people planted within the Department of Magical Transport. **If Potter
> Apparates or uses the Floo Network, we shall know immediately.’**
> 
> ‘He will not do either,’ said Snape. ‘The Order is eschewing any form
> of transport that is controlled or regulated by the Ministry; they
> mistrust everything to do with the place.’


  [1]: https://en.wikipedia.org/wiki/Harry_Potter_and_the_Deathly_Hallows
  [2]: http://harrypotter.wikia.com/wiki/The_Trace