If you're a visual thinker, the "shape" of an algorithm or data structure can be very helpful as well. Imagine it geometrically and think about how, say, the height of a tree compares to the length of a line with the same number of elements.
Of course, practice also helps. I'm lucky enough to get plenty of practice in school, but I think doing various condensed but nontrivial problems (think programming contests/project Euler) is probably both more fun and more practical for somebody out of school.
Ultimately, knowing running time of algorithms and behavior of data structures isn't really what's important; rather, it is just a "symptom" (in a good way) of having a solid grasp of what's going on. Just memorizing the times with flashcards is basically faking it--it might not be completely useless, but you'd be better off actually understanding everything.
I used to not have any idea about this sort of thing. My code worked fine, and I had no problems--I also never thought "hmm, I could have made this more efficient if only I knew about tree maps!". However, I now realize that the reason I never saw this was because I didn't know enough--I didn't even know enough to know I had a problem!
In short: you should learn how the algorithms and data structures work, not just for running times or interview questions, but to make you a better programmer. It definitely won't make you worse!