It's funny how our media chooses something a few times a year that can tell a story and scare the public.
It's not so much that they "choose" something. It's the fundamental difference between "news" and "not news" colliding with the way humans have evolved to give cognitive weight to things they hear about frequently and which can be associated with strong narratives.
C. dificile killing 16K people annually isn't news, because it's been happening for years. It's part of the background, not something which jumps up and begs to be called out. If a few thousand people in Africa had been dying at a steady pace from Ebola, for decades, it would also likely be part of the background... just like malaria is. Outbreaks are news, even if the death rates are small, while a steady year in and year out death toll is not, even if it's killing a lot more people. Unless, of course, there is news about initiatives to eradicate the "normal" disease, or interesting new research or something that makes a change worth talking about.
Ebola is also particularly powerful from a narrative perspective. The graphic imagery it produces, plus the horrific nature of bleeding to death from the inside out, makes for a strong story. Then when you add in self-sacrificing health care practitioners risking their lives and working in horrific conditions to try to help the sufferers, and then themselves suffering the same horrible death, it becomes a really compelling narrative. Throw in government corruption resulting in basic protective measures being unavailable to said self-sacrificing practitioners and it's a blockbuster.
C. difficile, not so much. People don't usually die of diarrhea, and it's an experience all of us are familiar with, and don't really want to talk or think about. Lousy narrative, no great changes to make it news, so it gets ignored, until someone decides to try swallowing human feces as a treatment. That's news, and it has a narrative we can all relate to and be disgusted by. Which is why we're talking about it now.
If you notice the stories that the media "chooses" to scare the public, they're all "news with a powerful narrative". These things resonate with people and get their interest -- including members of the media -- so the media provides them. The nice story plus the repetition of seeing the story daily causes people to dramatically overestimate the danger.
We all need to learn more about how our brains work so we can compensate for our inherent biases.