Ask him what it is he doesn't like about Matrix rules, and why he let you play one in the first place. Engage him in conversation, not confrontation, and try to resolve the issue. I know that I, for instance, often downplay Matrix activity in my own games (traditionally SR1-3, for the record) and simply got around it by running an NPC that handled most Matrixy stuff, letting my players focus elsewhere. Everyone, however, was told that going into the game, so no one made a dedicated pencil-neck squint Radio Shack refugee type who was only good in the 'Trix.
Everyone was happy, because everyone knew the score going into it. For him to let you make the character and then put his foot down, it makes it sound like maybe there was some misunderstanding about how the rules worked, some confusion about something that ended up working differently than he thought it would, or some incident that made him feel "trapped" or "tricked" or something. I'd discuss it with him and see if that's the case, to try and handle it.
That aside? If he does decide to downplay Matrix interactions, ask him if your current character can just take on "NPC" status, and still be the Shadowrun team's go-to guy for Matrix work -- but handle it off-site, be the voice in your ear giving the team tech support, and that sort of thing. He'd still be taken off-stage, and the Matrix wouldn't play as direct a role in the campaign, but without you having to see a player character killed for an OOC disagreement or misunderstanding.
Then, I'd speak with him very particularly about what he's looking for in player characters before spending much time and emotion getting heart-set on anything, with your next guy.
