Many beginning riders using flat pedals without toe clips tend to pdal with the instep of their foot over the pedal axle. That assures toe overlap since their foot is so far forward. I assume you don't do this.

If you are using "clipless" pedals and the overlap is small, you may be able to move the cleat slightly forward to avoid it.

Also, as noted, larger frames and cyclocross and touring frames all have more toe clearance. I have a 55 and a 57 cm Litespeed frames with the same nominal geometry (73° headtube and seat tube angles) and both with 170mm crank arms and identical pedals but the top tube is 1 cm longer on the 57. The 55 has toe overlap for me but the 57 doesn't. My 56 cm Surly Cross Check, doesn't have toe overlap problems even with fenders.