Yara said..
A properly designed fractional rig will have mast bracing to suit such as diamond jumper stays. Hence it will be just as strong as masthead, all other things being equal. However, some fractional rigs are intended to create mast bend, and the mast might be more flexible (read weaker) by design.
I don't know if more flex means it's weaker. Some devices as critical as airliner wings are designed to flex. It's a good way of spreading loads at times.
I can recall the legendary Lou Abrahams telling me that the Sydney 38 fractional rig was the most comfortable he had sailed with in his 50 years or so of ocean racing, partly because it flexed nicely in a seaway. I'm biased though, I wouldn't really have any other rig.