Yes, but those miners have invested so much capital into their mining hardware, software, electricity, etc that they have a strong incentive to make sure that doesn't happen. If an attacker were to gain control of 51% of the network Bitcoin would quickly become worthless or at least drop sharply in price making the whole attack pretty worthless. Not only is it very difficult to get to 51%, there are strong incentives for the relevant parties to make sure such a thing doesn't happen. If entire mining pools were hijacked with malicious mining software, someone would catch on and likely pull the plug on those machines before massive damage could be done.