Within the context of a paragraph, the sentence might be clear; but standing alone, the intended interpretation of the sentence is ambiguous.
Grammatically, the reader should look to the immediate antecedent of a pronoun to identify its meaning. The pronoun "they" is preceded by "men," so absent any other context the reader should conclude that women are fostering the belief that men are in charge. That said, I would advise an author to write so clearly that readers do not need to pause and deconstruct the grammar of a sentence.
If you are the author, I would recommend revising it. Here are some alternatives, each with nuanced differences in meaning — so choose carefully:
- Women have the ability to make a man think he is in charge.
- A woman has the ability to make men think they are in charge.
- Women have the ability to allow men to think they are in charge. [Still slightly ambiguous, but less so.]
- Like all women, she had the ability to make men think they are in charge.
- Women have learned to lead while allowing men to think they are still in charge.
Personally, I think the construction "have the ability" is clunky, indirect, and ineffective, so I would use an active expression like the final example above.
[EDIT: changed the last line to say "indirect" and "expression" rather than "passive" and "construction," as described in my comments.]