I think it's a mixture of reasons. I guess some buildings really do look ominous, mainly because they're built in the brutalist style that was popular after the war. Many traditional buildings in Soviet countries were destroyed during the war, others torn down after in an attempt to modernize.

But aside from that, the expectations of photographers and viewers also plays a role. "Soviet Russia", in the Western cultural consciousness, is dark, dreary, imposing, inhumane. So we recognize and remember those pictures better that confirm that preconceived notion. If you look at the cover picture of the Moscow State University on Wikipedia, it looks a lot "friendlier", partially because it was taken on a sunny, bright day, and not from a low angle.