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Unfortunately, one of the downsides of the automatic aspect of System Restore is that if your system gets a virus, trojan or such like, before your anti-virus or other security software removes the offender, System Restore backs it up. This effectively renders System Restore useless, because either restoring your system to a previous state can re-establish the virus or other malicious files you have removed, or your anti-virus program will (rightly) prevent you from reverting your system to a previous state (or other subsequent Restore Point) because the System Volume Information folder(s) (where Restore Points are saved) has a virus in it.
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