Strings in Python are immutable (can't be changed). Because of this, the effect of line.replace(...) is just to create a new string, rather than changing the old one. You need to rebind (assign) it to line in order to have that variable take the new value, with those characters removed.
Also, the way you are doing it is going to be kind of slow, relatively. It's also likely to be a bit confusing to experienced pythonators, who will see a doubly-nested structure and think for a moment that something more complicated is going on.
Starting in Python 2.6 and newer Python 2.x versions *, you can instead use str.translate, (but read on for Python 3 differences):
line = line.translate(None, '!@#$')
or regular expression replacement with re.sub
import re
line = re.sub('[!@#$]', '', line)
The characters enclosed in brackets constitute a character class. Any characters in line which are in that class are replaced with the second parameter to sub: an empty string.
In Python 3, strings are Unicode. You'll have to translate a little differently. kevpie mentions this in a comment on one of the answers, and it's noted in the documentation for str.translate.
When calling the translate method of a Unicode string, you cannot pass the second parameter that we used above. You also can't pass None as the first parameter. Instead, you pass a translation table (usually a dictionary) as the only parameter. This table maps the ordinal values of characters (i.e. the result of calling ord on them) to the ordinal values of the characters which should replace them, or—usefully to us—None to indicate that they should be deleted.
So to do the above dance with a Unicode string you would call something like
translation_table = dict.fromkeys(map(ord, '!@#$'), None)
unicode_line = unicode_line.translate(translation_table)
Here dict.fromkeys and map are used to succinctly generate a dictionary containing
{ord('!'): None, ord('@'): None, ...}
Even simpler, as another answer puts it, create the translation table in place:
unicode_line = unicode_line.translate({ord(c): None for c in '!@#$'})
Or create the same translation table with str.maketrans:
unicode_line = unicode_line.translate(str.maketrans('', '', '!@#$'))
* for compatibility with earlier Pythons, you can create a "null" translation table to pass in place of None:
import string
line = line.translate(string.maketrans('', ''), '!@#$')
Here string.maketrans is used to create a translation table, which is just a string containing the characters with ordinal values 0 to 255.