it is absolutely their choice whether or not to invite children to their wedding, but a bit misleading to talk about having children as flower girls
personally, though, i think children can really make a wedding. and that, whilst the bride and groom are of course the focus of it all, a wedding is about more than just a couple in isolation. it's about family, and celebrating with loved your ones, and so many of the people i love are children. i couldn't imagine not inviting children to my wedding, or knowingly preventing members of my family, or friends, from being able to go because they couldn't bring their children. at our wedding we had a bouncy castle and games for the children (and adults, lol!), to keep them entertained at the reception, and they were the first ones to get up and dance at the disco, breaking the ice for everyone else. apparently my nephew, who was 1 1/2 at the time, cried during the ceremony, but i didn't notice, and my bil took him outside until he calmed down.
of course, this is just my personal opinion, and i understand that not everyone feels that way, but those people will have to understand that not everyone will be willing or able to leave their children with someone else to attend their wedding, especially if it means being away for a couple of days.