Breathing magenta indicates that no user-firmware is running (safe mode). The system firmware still runs and can connect to the cloud, as to allow you to update your firmware. Breathing magenta can be caused by using the setup/reset combination, by flashing firmware that can't be run on the photon. That can be because it's accidentally compiled for a Core (make sure you target the Photon when compiling). Some strange errors can cause a user firmware not to be accepted (corrupted files). There's an inbuilt protection in the system firmware which verifies that the user-firmware is okay to run, if I'm not mistaken. Discrepancies between system/user firmware might also be a cause of malfunctioning. As long as the system firmware version is higher than the user firmware, you should be okay.
Just so I've said it; Although the Particle devices share a lot of similarities with Arduino, they are not actually Arduinos. They aren't some kind of 'special Arduinos', thus there is no 'normal Arduino'.
That said, I know what you mean, and yes, you can program them over USB similar to how you'd go about that with an Arduino 
You can download a compiled .bin file from the web IDE, and flash that using the CLI. You could also write your code locally and compile it on the cloud servers using the CLI. Alternatively, you could also set up a local toolchain, and use that to program it. The latter would also allow you to program the system firmware, opening up all the possibilities, and giving you the most flexibility, as long as you know what you're doing. You can then also use the latest firmware, which hasn't yet been pushed to the cloud, which may, or may not, contain additional features/bug fixes.
@mumblepins was kind enough to create an installer (for windows) that makes it extremely easy to set up the tools you need to get started. Have a look: