trumpetmike

When you speak, you use the sentence structure - which you understand because you have been speaking for some time and you are accustomed to using the structure to make sense. When you are playing a piece of music you need to apply similar rules, you need to make musical sense.

It is certainly one of the hardest parts of performing music, but in the same way that most people eventually learn how to make coherent sense when talking, it is possible for most people to make sense when performing music. It just takes time and eperience.

If you are finding this aspect of playing a piece more difficult than, for example, getting the notes correct may I suggest the following exercise.
Play the piece multiple times and breathe in various places - plan your breathing beforehand. Work out which of these breathing points make sense and use them in future sessions. Those that work are often not as easy to spot as those that don't, so you can reverse the process and simply eliminate all the options that scream out "don't breathe here" to you.

I totally agree with Rowuk's suggestion of singing - especially if you are working on more lyrical passages, being able to sing the phrase often provides an insight into what naturally works (many of my students find that this is easier if they put words to the music). I wish everyone would sing more, it really can make life a LOT easier.