Blame Anna Lear. ;-)
The colors used to be pretty much random and different on each site (since they were left unchanged when the new uniform top-bar was deployed), but they were recently standardized across the network. While this was being done, the actual color scheme was tweaked a couple of times base on community feedback, until it settled to the current scheme with blue for flags and brown for suggested edits.
Here's the specific feature request that led to the current color scheme. Personally, I kind of liked the maroon suggested edit notification color we had briefly, but I'm not going to start demanding that we repaint the bikeshed once more. The current color scheme works (unlike, say the black on black we used to have here on meta), and that's good enough. Besides, you can always change it with a user style sheet.
- Reputation change = green background.
- Normal inbox = red
- Moderator inbox = blue
- Flag review = blue
- Suggested edit review = orange