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Often times, the hack is through a web front-end. Back-end systems (such as DBs) are heavily firewalled, logged, monitored, etc. and are generally very well protected. Systems guys (OS and DB) know security pretty well and have been doing it for a long time now.

Much of the web software that powers the front-end is complex (PHP, Java, .Net, JS, CSS, SQL, includes, 3rd-party libraries from everywhere, etc). That complexity has a broad attack surface that is difficult and time consuming to test. And many devs are late to the security party (unless we're talking OpenBSD developers).

Management wants to push out new features by X date. Devs have very little time to test and are behind on security anyway. Hackers have all the time in the world to poke at the web front-end and test every possible combination of things until they finally get in.

In a nut-shell, that's the problem as I've seen it.