Dowel joints get a bad reputation in furniture, and they are misused a lot. I was process engineer for a high volume door operation that used dowel joints, and they worked great. They are very accurate, so coped joints seat weather tight; and they withstand severe tests in wind load, impact, and cycle slam testing. As gmercer points out, grooved dowels and brad point bits are important. The old rule of thumb that penetration of 3 times diameter gives a joint where the dowel will break before it comes unglued is valid from my experience, and I've tested dozens of stile and rail doors to structural failure. True dowel drills are also back taper ground 0.001" per inch of shank so they don't burn in the cut, and this is also improves glue adhesion.
I do dowelling in my own shop with a bench top drill press and a vertical table that clamps to it. The dowel holes are bored in the rail ends while still square cut, then the coped ends are cut, and finally the sticking moulding. The joints need to look perfect. Dowels are a drive fit; and once they are started, there's no going back.