First of all, all of these commands make perfect sense to me. I don't know why exactly, but I've never used a version control system that made more sense than this. I never really felt like I'm home with Perforce and SVN. Neither with Mercurial, although Mercurial is better than most.
git remote rm
This deletes the reference to a remote repository. The difference between Git and SVN here is that in Git you can have
multiple remote repositories with which you can communicate.
This comes in handy when pulling and pushing to/from multiple people. Imagine swapping code between you and your colleagues, doing experiments, doing code reviews, and so on. It also comes in handy when you're dealing with Heroku, or when you've got an "open-source" core that's pushed to GitHub and another branch with proprietary additions that you push somewhere else.
Also, all commands for managing these repository references start with "git remote" and to find out how to do something with them you just do "man git-remote".
git branch -D
This deletes a local branch. It has nothing to do with the above. It does not use "rm" because that can be the name of a branch and this command is heavily overloaded.
git tag -d
This deletes a tag. It is consistent with the above command, as "git branch -d" (lowercase D) is also supported, but uppercase D means that the deletion is forced, even if the branch was not merged. Again "rm" was not used, as that can be confused with the name of a tag.
git rm
Deletes a file, but you don't have to use it. If you're confident about your editing skills, you can just commit all the deletions with "git commit -a ..." ... git will also be smart enough to detect a file rename, even though you did a deletion + addition.
"rm" is also the name of the command that does the same thing in Unix, being associated with the removal of files.
git remote rename old new
As I said, "git remote" manages references to remote repositories. This just renames the reference named "old" to "new".
You could say that they should have used "mv", like in the case of "git mv", however this is not a "move" command. This is just plain renaming.
git branch -m old new
This renames the local branch named "old" to "new". It is indeed inconsistent with the others, but that's because the "git branch" utility has been overloaded a lot. This command does confuse me from time to time.
git mv
Like in the case of "git rm", this command does a "mv", while registering the action in Git. It is also not necessary if you're doing a "git add . && git commit -a".
"mv" does make sense here, as it is the name of the Unix command for moving files.
And a final tip for beginners: use the "man" pages. In a terminal input any of the following commands when you need help ...
man git-remote
man git-branch
man git-tag
man git-rm
man git-mv
man git-push
man git-pull
man git-reset
man git-checkout
etc...