It usually doesn't matter much, but there are some situations where it can matter a lot. For one thing, you can't use seek() on a pipe, so e.g. `cat bigfile | tail` has to read through the entire file to find the end, but `tail bigfile` will read the file backward from the end, completely skipping the irrelevant beginning and middle. With `pv bigfile | whatever`, pv (which is basically a pipeline progress indicator) can tell how big file is and tell you how for through you are as a percentage; with `cat bigfile | pv | whatever`, it has no idea (unless you add a flag to tell it). Also, `cat bigfile | head` will end up killing cat with a SIGPIPE signal after head exits; if you're using something like "Unofficial bash strict mode" [1], this will cause your script to exit prematurely.
Another sometimes-important difference is that if there are multiple input files, `somecommand file1 file2 file3` can tell what data is coming from which file; with `cat file1 file2 file3 | somecommand` they're all mashed together, and the program has no idea what's coming from where.
In general, though, I think it's mostly a matter of people's expertise level in using the shell. If you're a beginner, it makes sense to learn one very general way to do things (`cat |`), and use it everywhere. But as you gain expertise, you learn other ways of doing it, and will choose the best method for each specific situation. While `cat |` is usually an ok method to read from a file, it's almost never the best method, so expert shell users will almost never use it.
Another sometimes-important difference is that if there are multiple input files, `somecommand file1 file2 file3` can tell what data is coming from which file; with `cat file1 file2 file3 | somecommand` they're all mashed together, and the program has no idea what's coming from where.
In general, though, I think it's mostly a matter of people's expertise level in using the shell. If you're a beginner, it makes sense to learn one very general way to do things (`cat |`), and use it everywhere. But as you gain expertise, you learn other ways of doing it, and will choose the best method for each specific situation. While `cat |` is usually an ok method to read from a file, it's almost never the best method, so expert shell users will almost never use it.
[1] http://redsymbol.net/articles/unofficial-bash-strict-mode/