Flowers are easy to control if you take precautions , but if you don't box them in and it rains/snows, then yeah, they'll grow out of control. But at the very least, they're not nearly as intrusive as Bamboo was in New Leaf.
They key thing about flowers is they can spread to an adjacent tile in all 8 directions (including diagonals) as long as that tile is Grass or either type of Dirt, and is not occupied by any item. Any other type of tile, including paths, patterns, or sand, will not allow flowers to spread. I will clarify though, that although flowers won't spread to sand, you can replant already grown flowers in sand and they won't spread.
A common tactic is to use the "invisible" pattern that was mentioned earlier in this thread. You basically just paint a pattern with the transparent effect, so when you lay it over grass, it will still appear to be grass but flowers won't be able to spread to it. It's really simple if you don't want a specific path/pattern/etc. to block the way.
