I Put two new speakers in my car an they played for like 5 minutes an then shut off an my cd player started saying protect an wont play. how can i get it working again?

Either your speakers are mismatched to the unit or they are wired incorrectly.
Speakers connected to each of the output channels of this unit should be between 4 and 8 ohm and more than 50Watt
To get the unit working again disconnect the speakers and make sure there are no short circuits present at the connections. Verify that the speaker to be connected is more than 4 ohm impedance. This is printed on the rear of the speaker. If it is less than 4 ohm it cannot be used unless together with another speaker connected in series.
Lets assume you have 2 ohm speakers. One wire of one of the channels gets connected to the + of the speaker. The other wire of the same channel gets connected to the - of the other speaker. The connectors on the 2 speakers that have not been connected till now gets connected together. In this way you get 2ohm+2ohm=4ohm which is safe for the unit.
Now of course you'll need another 2 speakers for the other side!
Leave a message if you need further assistance and I'll get back to you ASAP.

Protect means the speakers are drawing too much current. Recheck your installation to make sure the wires are not shorting to each other or to the chassis. If the wires look good, check the impedance of the speakers using an ohmmeter. Anything less than 4 ohms is probably a bad speaker, but compare your readings to the spec on the box. Please let me know if you have more questions, and thanks for using FixYa.