Taking YouTube links out of a list of GitHub repo READMEs
Here are some concerns/suggestions:


you are reading the file twice - once to get the row count and when reading the links. And, you don't need to initialize the csv.reader to get the row count, simply use sum() over the lines in the file. You would probably need to use infile.seek(0) after getting the count and before initializing the csv reader
use _ for the throw-away variables (when counting the number of lines)
if len(ids) == 0: can be simplified as if not ids:
it looks like you don't need .findall() and should use .search() method since you are up to a single match
if there is a single repository link per line, you probably should have get_repository() method instead of get_repositories() and avoid the for repo in get_repositories(row[3]): loop - remember, "Flat is better than nested"
instead of handling the enumeration with row_counter manually, use enumerate()
instead of accessing the current row fields by index - e.g. row[1] or row[3], you can unpack the row in the for loop, something like (an example, I don't know your actual CSV input format): 

for index, username, _, github_link in reader:


Or, you can use a csv.DictReader - accessing the fields by column names instead of indexes would improve readability - e.g. row["github_link"] instead of row[3] 
you don't have to convert the args to a dictionary - return args and then access the arguments using a dot notation - e.g. args.filepath