there are certain spots that are more conducive to transmission than others, and these are the places the squiddies look for. it also has to do with detection, as, if they were to broadcast from just anywhere, it increases the chances that squiddies will find them. And there is the fact that, certain spots in the tunnels may be not conducive at all to a signal, which would be the equivalent of losing reception on a cell while passing through a tunnel; aka the ones jacked in would die.
i agree with jedi... i think their broadcast signal can be compared to a cell phone's... it's just better in some places... but if there are areas that are better for broadcasting wouldn't the machines send more sentinels to patrol the area..?
If they could enter the Matrix anywhere, then why not do it in the safety of Zion, instead of losing 3 three ships. But that wouldn't of been as fun, so Jedi's theory makes sense.