Is encrypting credit card numbers one by one with rsautl secure?
As long as you use a secure padding mode (i.e. -pkcs or -oaep, not -raw).  The default padding mode for openssl rsautl is -pkcs (i.e. PKCS#1 v1.5), so you should be OK.  That said, OAEP is recommended over PKCS#1 v1.5 padding, so you might want to use the -oaep switch.