I know a dog that was born of a german shepherd, but fathered by a chiuahua. Conversly, our puppy comes from a cross between a queensland and a cockapoo. Maybe size really doesn't matter as long as you know how to use the tool you have?
All that would be required for fertilization to occur would be that one of his "swimmers" found one of her eggs and penetrated through the cell wall and it really does only take one. The fact that his anatomy is the smaller of the two really makes that completely believable in terms of possibilities - she doesn't even have to have felt anything for fertilization to be successful.
However, biologically, usually animals from two different species have the wrong numbers of chromosomes to result in offspring. The fact that a giant and a human can inter-breed would indicate that either:
- We are actually of the same species but of vastly different sizes (as in the dog example I offered), and they simply over came the size differential either through magic using spells to make one or the other a different size, or the size differential didn't actually pose a problem for them.
or
- The two species can have an offspring, but that offspring will never successfully produce its own offspring (as in the case of mules which are bred from a horse and a donkey and always come out female and infertile. This kind of a result happens, but amongst animals is extremely rare - most of the time, cross species intercourse is quite literally fruitless.
So, my problem with this pairing is less about size issues (seriously, he was a wizard - he had magical options here - as listed by others) and more about the chromosomal difficulties in the match. It helps that niether Hagrid nor Madam Maxime went on to have children of their own in determining that perhaps the second option here is the case making it less of a "hole" if it ever was one.
In either case, I don't really believe the size differential actually poses a problem to inpregnation, though it may have created a problem in Hagrid's Mother's enjoyment of the process.