This sentence is technically ambiguous, but it is typically interpreted as an indirect passive sentence with some implicit subject. Let's assume the implicit subject is 父親, and compare your sentence with a typical indirect-passive sentence:
- 私は財布を盗まれた。
I had my wallet stolen.
- [父親は]私を取られた。
[My father] suffered on account of me being taken. / [My father] was deprived of me.
A sentence like 1 should be found in any textbook. And this is why を is used instead of が here. The subject of this sentence is not 私 but someone else mentioned in the previous context!
Note that に in 人質に is almost certainly a role marker rather than an agent marker in your sentence. This part requires common sense rather than grammar; it is unusual for a hostage to kidnap someone.
- 私は財布を泥棒に盗まれた。
I had my wallet stolen by a thief.
- [父親は]私を人質に取られた。
[My father] suffered on account of me being taken as a hostage.