I have a 2006 PT Cruiser and when I turn the car on in the morning I hear a rattling noise on the right front on the passenger side under the hood and then the check engine light start flashing.

Since check engine light is flashing, get the code scanned, that will tell you what's happening. (if you can't start or drive car, then try borrowing, renting or buying a scan tool.) The "rattling" noise might be a relay or solenoid. A solenoid connected to the cars EVAP system might prevent it from starting.

y PT Cruiser still crank up but first thing in the morning you can hear that rattling noise and the engine light is still on but its not flashing anymore. I can still drive it but is it safe to drive?

If light flashes or stays flashing, it means there's a timing issue and potentially damaging to the engine. Again, take it to a parts store and get the code scanned, it's free, or take it to a mechanics and get a thorough diagnoses. Without knowing what the noise is or codes are, I can't really make any other suggestions.