Bathroom fan intake location
Only caution would be if it's actually in the floor, in which case you might want to consider precautions from liquid water going into it. Down low it won't vent moisture as well, but since that's not a concern for you it should not matter much - right behind the toilet bowl would appear to be your ideal intake position. Negative pressure is fine in ducts unless you are using a jet engine rather than an inline vent fan.