First of all, I would avoid using these "static" methods that all get called from main. Rather, have the main method instantiate your class and call a method on it, and then have all other methods used not be declared static. For example:
Methods should be declared private unless there is a reason to not declare them private. The method countCommas has no access modifier, so it is protected, not private.
I don't think countCommas should declare that it throws an IOException
You catch IOException here. You could also move the lines above (that may throw IOException) into this try block.
So it can't throw any IOException.
Speaking of exception handling - displaying the stack trace is rarely the correct way of doing so.
The user doesn't want to see a stack trace. It means nothing to them, and it exposes some of the code internals which isn't a good thing.
Rather consider - why would an IOException be thrown and what does it mean for the user? How about FileNotFound exception, what does that mean to the user? How can you tell them what went wrong in a nice way.
I don't like this line.
What is the meaning of 44?
Of course I know what the meaning is because I know ASCII but others might not.
If you have to use a number like this, at least make it a named constant so it shows its meaning clearly. You could also probably say i == ','. Not entirely sure if that'll compile but it's worth trying.
This code would just display a number to the user. What does that number mean? You could say: System.out.println("Number of commas: " + count);
This comment is unnecessary.
Not that there's anything wrong with this, but why not just use a Scanner? It's probably simpler.
Actually you could use a Scanner for reading the file too, instead of a FileInputStream. Scanner is the simplest solution for text-only files.
I would add Javadoc comments on this, explaining the intention of the code, assumptions, etc. Anything that's useful to know about it.
General comment: this method could be split into two. One method to prompt a file, and one to count the commas from the file.
This readLine is entirely unprompted. If the user runs this application, they will be greeted with a blank screen.
Instead, prompt them:
System.out.print("Enter a filename to count the commas of: ");