Because it's powerful. It also has some quirks that have been inherited from old versions, but they're not too hard to work with.
Where are you struggling with?
The basic premise is you grant access, not prevent access. Most people get in trouble by thinking about restricting access to a particular group of users.
Did you already read our overview doc on JIRA security? I believe this doc is the first thing you should read to understand JIRA security:
https://confluence.atlassian.com/display/JIRA/Configuring+Security
Cheers!Teilor
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