A note about how I handle cover: I'll let you benefit from cover even if you haven't reused the Take Cover action at the end of a pass. If you haven't exposed yourself since last taking cover (for example, you've been reloading or taking a drug) you get all the cover's bonus. If you have exposed yourself since last taking cover you'll get a reduced defense bonus if you were in good cover (as described on pg 190).
For example - balaclava last took cover a couple passes ago and has exposed himself (by shooting) since then. He won't benefit from good cover because he's exposed himself but it's not as if he had to totally step into the open to shoot. So he's still benefiting from partial cover.
Here's a table to help illustrate what I mean:
[table="width: 500"]
[tr]
[td]What happens when you don't retake cover at the end of a pass[/td]
[td]Partial Cover (+2 normally)[/td]
[td]Good Cover (+4 normally)[/td]
[/tr]
[tr]
[td]Haven't exposed yourself since you used Take Cover[/td]
[td]+2 defense[/td]
[td]+4 defense[/td]
[/tr]
[tr]
[td]Have exposed yourself since you used Take Cover[/td]
[td]+0 defense[/td]
[td]+2 defense[/td]
[/tr]
[/table]
If your action is hostile (such as shooting, taking aim, or whatever) it's going to count as exposing. Reloading and the like won't expose you. Actually moving out of the cover at all (using your movement) will totally strip you of cover, of course.
Most of the cover in the subway train is good cover - it's big metal panels and heavy benches for you to duck or crouch behind.