Toilet repeatedly clogs - is putting toilet bowl cleaner in the toilet's tank causing the problem?
If by "clog" you mean


You try to flush,
Water flows into the bowl,
The water level stabilizes higher than the normal resting level and the toilet doesn't actually flush. 


Then I really can't imagine any way the cleaner fluid could be causing it. 

In any case, check the directions on the cleaner product in question. It's certainly possible for an improperly used cleaning product to cause other problems in in a device like a toilet; I'd specifically be worried about some of the soft or hinged gaskets degrading.