SEGA has had success in the PC market, but as you've said it has been largely due to acquisitions. The Total War series was already successful when SEGA started publishing the franchise, Football Manager had already see a decade of success under Eidos (though it was known as Championship Manager), and Company of Heroes had the benefit of THQ's support.
In short, while all of these games have done well for SEGA, they would have done well for ANY publisher that picked them up. So I'd say that this has less to do with SEGA being very good at selling games to the PC market and more to do with SEGA simply being smart enough to acquire winners for that market.
SEGA definitely HAS a future in PCs, but I'm not sure if that really is there future. Unless there future is just Total War, Football Manager, Relic's stuff, and any other big PC devs SEGA picks up. I think the major issue for SEGA has always been a lack of faith in their own franchises outside of Sonic and Yakuza. I've never seen any other SEGA IP get the kind of advertisement that, say, the original BioShock or Deadspace got. Until SEGA is willing to take THAT kind of risk and actually back some of their other IPs with serious advertisement dollars, their future isn't any one platform: it's just wherever their big IPs already do well.