All of the big bicycle manufacturers in the USA now offer road bikes designed just for women riders. The four largest are Trek, Specialized, Giant and Cannondale. Of the four, Trek and Specialized take the women's market very, very seriously. They offer women's road bikes for everyone from entry-level to racers, for all budgets and with many component groups to choose from. There might be a lack of "wow factor" with bikes from the big companies (the name just doesn't carry the status or appeal of a boutique brand) but the ride quality of the bikes is definitely world-class. Every year, there are more and more women's bikes to choose from.
Even with the wider range of frame and component options available now, women still sometimes have to deal with bikes outfitted with second-tier components. Women may find a bike that has the same frame quality as the comparable men's model, but the components are a step down. It's an example of the inequality still present in the sport. Many bike manufacturers have made big strides in embracing the women's market, but they're not quite there yet!
It can still be difficult to get a female-specific bike from small manufacturers who only offer stock frames (not custom); that said, small "boutique" bike builders may use frame geometry that is female-friendly. Most women definitely fit better on a female-specific bike with a shorter top tube, narrower handlebars and women's saddle. Some "unisex" bikes tend to run relatively short in the top tube - so if a manufacturer you're interested in does not offer a women's bike, get sized on their bikes anyway. You may be surprised!
Of course with custom frame builders it's no problem to get a bike that will be a perfect fit for the woman rider.
The most important thing is to have a bike professionally fitted for your individual needs. There is simply no reason to ride a poorly-fitting bike.