Inserting the salt (yes, it must be talked about), and iterating the function at the same time, is a bit more tricky than what it usually appears. In particular, a hash function such as SHA-256 is not exactly a "random-oracle-like" function; it exhibits some internal structure. Any homemade construct could hit one of those fine details from which deadly weaknesses may emerge.
Making sure that you did it right is difficult, just like building any cryptographic algorithm. That's where bcrypt is better than any homemade construct: bcrypt has been published and in use and presumably inspected for flaws by many people over quite some time. This is basically the only hard measure of security that you can get in cryptography. The generic advice of "do not define your own algorithms" applies here too.