On Unix systems a file can be hidden from ls and other applications by prefixing the filename with a period. This was introduced in Unix Version 2 as a side-effect of adding files . and .. to support the new hierarchical filesystem. To avoid these navigation files appearing in every directory when ls was executed, filenames with the first character '.' were filtered out. This unintentionally hid other files with this prefix. Once this precedent was set, other programs implemented the same behaviour, which continues to this day.
More details on this can be read in Rob Pike's Lesson in Shortcuts.