Linux security has kind of had two things going for it for a long time. Linux kind of had security through obscurity, because even though it's open source, not many people have used it until recently, so it was more valuable to target Windows systems. Secondly, since Linux is open source, any flaws that malware did exploit to gain a foothold were quickly patched, making the malware useless. So a Linux malware developer would end up developing a piece of malware for a less commonly used system that would get patched faster, making it nearly pointless to do so except against extremely high value targets.