It really depends on the reader you have, but in my experience they fall into two main groups:
Those that appear as an HID device - a keyboard.
Those that appear as a serial port
I can see that the "progmac" device you mention is the former - it appears as a keyboard.
Those that appear as serial ports are actually easier to integrate into projects. Reliably reading from the standard input that is the device, and not the standard input that might be a real keyboard or ssh session, can be a pain. However, if it is a serial device you can simply open a connection at the right baud rate and talk to the unit.
On the Pi I could have used USB - though in fact I ended up using the UART on the GPIO pins, so that I could leave the USB free.
This worked fine, but you have to be careful, since these pins run at 3v3 logic - 5v logic can damage them.
Also, by default this is a serial console, wheras you want to use it for a device. This post:
http://raspberrypihobbyist.blogspot.co. ... -port.html
Explains how to do that
This is the kit I used:
http://www.ebay.co.uk/itm/13-56MHz-RFID ... TQ:US:1123
I have also used one of these:
http://www.ebay.co.uk/itm/RFID-ISO14443 ... 2eca279be3
Which worked just as well, and appears as a USB COM port rather than bare TTL serial - so easier to use, but less easy to nicely integrate into a product.