From an interview with the directors:
Sinclair: Why were they only able to jack in through hard-lines, but still able to communicate over cell?
WachowskiBros: Sinclair, good question! Mostly we felt that the amount of information that was being sent into the Matrix required a significant portal. Those portals, we felt, were better described with the hard lines rather than cell lines. We also felt that the rebels tried to be invisible when they hacked that’s why all the entrances and exits were sort of through decrepit and low traffic areas of the Matrix.
The full interview: https://www.matrixfans.net/movies/the-matrix/wachowski-broth...
More speculation by a fan about this: https://screenrant.com/matrix-phone-hard-line-enter-exit-exp...