In multi you do have a big problem, since BtRL is based on Freespace_open version 3.6.9, which has a rather inefficient networking backend, which in turn means high lag. Basically the lead indicator is off in MP, and the higher the lag you're experiencing, the further ahead of the lead indicator you have to aim to actually hit things. It takes some practise to get right, and even then it's still much harder than SP.
In SP, the lead indicator is correct. However, it doesn't take into account the positions of your guns, only the time it'll take the rounds to travel the distance to the target. This means that on a Mk-VII, for example, with a gun in each wing and one in the tail fin, you can be aiming perfectly at the lead indicator and yet have your shots go above, to the left and to the right of the target instead of connecting. Try using the rounds themselves as tracers and walk the fire from at least one of the guns on your ship onto the hull of the enemy, instead of blindly relying on the lead indicator. Sometimes just rolling your ship a bit will also be enough to bring round onto the target. Finally, try not to attack head on all the time - Ships present a very small profile from that direction, so try to target them while they're in a turn so you can get them from above or below where their profile is mugh larger.