When talking about macro lenses I think you'll find that they are most typically referring to using it at its highest magnification, typically 1:1. Simply, 1:1 magnification means your subject will be projected on to the sensor/film at the same size as it actually is. That means that on a full-frame sensor DSLR your subject is about 36 x 24 mm (about 1-1/2 x 1"); on a APS sensor DSLR your subject is about 23 x 15 mm (about 1 x 0.6").

A short macro lens, used at 1:1, does put the subject very close to the front of the lens because of how small it is. Working distance can be just a few inches and that can be too little space to light it adequately.

Back up for a moment, though -- figuratively and literally. Many, many flowers are notably larger than 36 x 24. I have a variety of lilies growing around me and most of them are significantly larger than that. When shooting those flowers I am not going to work for a 1:1 magnification because it would not include the whole flower (or majority!) in the frame, and in fact turns into a more abstract study. (Fun and interesting in itself, however!) So, back up to fit the flower in the frame and you'll find you've got a lot more working distance. You might be shooting at a reproduction ratio of 1:2, 1:4, or greater.

The very small working distance of short macros can indeed be a challenge, but for flowers that wouldn't be a big concern for me. That said, I think something in the 100mm focal length range is far more flexible and useful for a macro lens.