@Stainless Steel Devil Rat touches on an important point here; cost.
Corporations are all about the bottom line, and in Shadowrun pretty much everything in society is wireless; the can you're drinking from has wireless RFID tags in it so that it can show you targeted ads for the other products sold by the vendor while you're enjoying your favourite carbonated beverage, your coffee maker is connected to the Matrix to that it can predict when you'll wake up by communicating with your wireless biomonitor in order to have that steamin' hot cup of soycaf ready when you walk into the kitchen, and so on and so forth ad nauseum.
Consider then, that running fiberoptic cables through concrete walls and rock and dirt ground is WAY more expensive than simply putting a camera on a pole and hooking it up to the Matrix. If you're a mid to large size corporation you can afford expensive hosts that protect your devices, right? And the megacorps controlling keep implementing security protocols to keep all the bad hackers out, right? Because they surely wouldn't sell you stuff they knew could easily be compromised, right?
Sarcasm aside (and that is an in-world explanation, not directed at anyone here by the way), the Matrix revolutionized the way the world works. If you go back just 50 years in our world and talked to people about the basic premise of the internet, they would probably have the same questions as you. "Surely, this is insecure and ripe for exploitation!?"
Well, yes. But the damage inflicted by the minority is so outweighed by the net benefit from a wireless network, and, most importantly, the corps operate shadowrunners as much as, if not more, than anyone. It is directly against their own interests to keep everything offline, because the corps needs to have an ability to infiltrate, sabotage, and/or otherwise subvert the security of their opponents as they need to secure their own sites and systems.
Think of the Matrix as a form of a symbiotic relationship; all sides gain something in the exchange.