The answer is…it depends on the song.
In many cases, improvisation over tonal harmony (that is the movement through and definition of different keys within a song) is taught using modes.
There isn’t one musician from Jelly Roll Morton through John Coltrane I’m aware of who learned how to improvise through tonal harmony using modes.
Although Coltrane, Miles, Bill Evans and many others after them expanded the landscape of form and harmony to include the pre-harmony modal approach as a vehicle to improvise jazz on, they explored and in Coltrane’s case exhausted tonal harmony or “changes” before moving on to the modal approach. This is the best model for a well balanced musician.
To achieve this, both approaches must be learned individually. Use modes when improvising on modal music but NOT when improvising on common standards or other songs. For tonal harmony you must learn how to connect lines and outline tonalities within the construction of your melodies. Make cadences and play phrases.
After a fluidity on changes has been established the superimposition of modal applications on top of tonal harmony can be explored. The greater one’s comfort level within harmony, the more effective they can be when being adventurous and playing more creatively. Examples of players comfortable doing this are Bob Mintzer, George Garzone and many of today’s players.