To answer your questions:
Is this safe to run?
Depends on your definition of "save". It will not wreak havoc, but I wouldn't recommend it.
... does rm skip the trash?
The rm command skips the trash. rm doesn't even know about the concept of recycle bin. Virtually all command line commands have no idea about the concept of recycle bin (some oddballs think it is fun to have a terminal based recycle bin).
If you insist on a cron job to clear your download directory I would recommend doing it like this:
find $HOME/Downloads/ -mtime +1 -delete
This will delete all files (and directories) older than one day. Otherwise, if you downloaded something on 8:59, it will get deleted right away.
Note: under linux the wildcard *.* means something else than under windows. I assume you come from the windows world where *.* means every file.
Observe:
$ ls
foo foo..bar foo.bar foo.bar.baz
$ echo *
foo foo..bar foo.bar foo.bar.baz
$ echo *.*
foo..bar foo.bar foo.bar.baz
$ echo *.*.*
foo..bar foo.bar.baz
$ echo *..*
foo..bar
* gets expanded to everything, including ., except a leading ., but that is an entirely different story. *.* gets expanded to everything which has at least one dot in the middle. *.*.* gets expanded to everything which has two dots. I think you get the idea, the dot doesn't have any special meaning in filename expansion. Be carefull though, the dot has a very special meaning when dealing with regular expressions, but that is also an entirely different story.