It makes some things more difficult. CD/DVD's are generally used instead. Sometimes other computers could be connected but in that case there would be some organizational procedure for attempting to make sure that other computer was as low risk as possible.

You can't eliminate the possibility of malicious action, Stuxnet proves that. It's my opinion that at least for critical infrastructure we can probably make things much more difficult for our adversaries at a relatively low cost. This pipeline is purported to carry half the gasoline/diesel/heating oil to the east coast, but I'd be lying if I said I knew exactly where the cost-benefit equilibrium should land.

I'd be lying if I claimed I knew...but I would be willing to bet that cost-benefit analysis was made a long time ago before these concerns became so timely.