Let me start off by saying that netrunning, while definitely a cool concept in SciFi games, makes for some really bad game design, exactly because of the reasons you state. It takes the majority of the party out of the game.
A key question here is
At what speed does hacking work?
Speed of thought
There's not much you can do. The other players' characters are frozen in time, and might as well go get Pizza, since they're not playing anyway.
The only remedy here is to minimize the time spent netrunning by removing longer runs completely from the game, and reduce them to 5-10 minute runs. That might leave the player of the runner unsatisfied, as he is largely denied his spotlight.
Another option would be to incorporate the other PCs into the hack-world as well, at which point it becomes a fully-fledged parallel universe to play in, where the squishy hacker that can't hit a barn door with a laser rifle if the stands 2 feet in front of it turns into the most potent of characters, while Hulk Hogan can't open a door.
Be aware that if Hacks take a considerable amount of game time (i.e. several hours of play), this is an extremely long amount of spotlight time for the hacker, which might annoy the other players (even if the average spotlight time for each player is equal). This is the same reason you mix monsters, traps and riddles in a game with a warrior, a scout and a scholar, where the players of the latter two might get bored if you fought hordes of monsters for 3 hours straight, even if the fighter-player enjoys it. It's potentially drastically worse, depending on the amount of uselessness of "non-native" characters. So if you go this route, be extremely careful not to annoy the other players.
Regular game speed
If netrunning takes real-life time, your options are much better, because you can incorporate the hack-job into time-critical/parallel scenarios, the simplest of which being a real-life fight. Some options for your hacker include (but are not limited to)
- Disable (or take over) that Auto-Turret/Deathbot before it tears the party to shreds
- Override a locked door to allow the party to escape after a successful (but for reasons of suspense not alarm-free) heist
- Get that data out of the mainframe as long as your colleague flirts up the guard
- Reroute the security camera footage just long enough for your infiltrator buddy to sneak past the guard patrols
With such parallel encounters, everyone can play at the same time, with multiple spotlights, so everyone is happy (ideally).