The method for hiding files that you do not want showing up in the Tree View (which is what most people mean when they ask this question) depends on whether or not you've added the files to your .gitignore. If you have, then all you have to do is:
Open Settings
Scroll down the list on the left to find the Tree View package
Click on it to bring up the package-specific settings
Ensure Hide Vcs Ignored Files is checked
If you want to hide certain files in the Tree View whether you have a Git project open or not:
Open Settings
Add the file mask to the comma-separated list under Ignored Names (add *.pyc in your case)
Scroll down the list on the left to find the Tree View package
Click on it to bring up the package-specific settings
Ensure Hide Ignored Names is checked
Also note that when you add a file mask to the list of Ignored Names that files matching that mask will not show up in other parts of Atom like the fuzzy-finder:find-file (Cmd+T on OS X and Ctrl+T on Windows/Linux by default) command.
In Atom 1.25.0 on Ubuntu I found this setting Hide Vcs Ignored Files under packages configuration: Preferences -> Packages -> Tree View -> Settings.
Also, pressing I while Tree View activated also works for me (@Suraj Thapar's comment).
Please note, you have 2 options here: Ignore file by .gitignore and ignore files by Hide Ignored Names which refers to Ignored Names core config settings.