You can do something like:
total_lines = 0
matched_lines = 0
for line in open("filename"):
total_lines += 1
matched_lines += bool(re.search(r"\b[A-Z]{3}\b", line))
print "%f%%" % (float(matched_lines) / total_lines * 100)
Note '\b' in search pattern -- it matches empty string in beginning or end of word. It helps you to prevent unwanted matches with acronyms longer than 3 ('asdf ASDF asdf') or with acronyms inside word ('asdfASDasdf').