Yes, Malaysia is a pretty safe country, and its security is almost as good as that of Singapore. Remember that Malaysia or Singapore has extremely strict laws. Many violations, including carrying a tiny amount of cocaine etc... are subject to capital punishments by hanging or firing squads, and these contribute to the stability and security in these 2 countries.

Don't compare Malaysia or Singapore to other Muslim countries in South East Asia. One such example is Indonesia - the most populous Muslim country in the world and one of the most unsecure and unstable countries nowadays.