We need a lot more detail about exactly what you are referring to here. Specifically, specify "a SSL Cert" where exactly?
Also, nothing "uses" certs in the trusted root store. Those certs are there to establish a trust with a PKI and are from root CAs that define those PKIs. When a system attempts to use a cert, one check that is performed is whether or not that cert was issued by a PKI (aka CA chain) that is trusted which is, as noted, defined by the certs in the trusted root store. Thus, is the PKI is not trusted, the cert is considered untrusted.