Women in general can fly as well as men, and you will not have any gender problems (other than possibly getting hit on by co-workers) at the airlines, especially the larger ones.
You might run into a few old-school types in the charter/corporate world...the smaller operations don't necessarily provide the sexual harrassment training and enforcement found at larger operations. Also be aware that in these jobs you might get hired just because the pilot you will be flying with wants to hang out with you on layovers...make sure you know who you will be flying with and are comfortable with them on a personal and professional level.
It is worth noting that there is some lingering resentment due to the fact that airlines (and the military) hired under-qualified females in the past and attempted to train them to proficiency. Said extra training often doesn't work, and there were a number of high-profile crashes. Nowadays most airline employment is based on merit alone, although you might get called for an interview sooner if you are a female. The aviation culture evolved out of male/military roots... just keep your sense of humor and you should be in good shape. All of my female friends in aviation are progressing just fine, they seem to complain about the same stuff as other pilots.