They made Hugh Jackman Wolverine based on the Ultimate Marvel version who is significantly taller than the 616 Universe version.
Likely the other way around, since Ultimate Wolverine didn't show up until like two years after Jackman was cast in X-Men.
But yeah, I initially had a problem with Jackman's casting. I think Hugh Jackman was excellent and made the role his own, but a big part of what made Wolverine a unique character was that he was underestimated or dismissed by some foes due to his stature, repeatedly called a runt by them, he didn't give a shit, he'd carve them up anyway. Nobody's going to underestimate Jackman Wolverine. Comic wolvie also wasn't good looking at all, bordering on ugly... and despite all of those disadvantages, he was the probably the 2nd most popular Marvel character at the time.
Basically, it was the equivalent taking Captain America and turning him into a super short, ugly dude. Being tall, good looking, and physically perfect is inherently part of Captain America's character.
In the end though, I didn't have a real problem with it because Jackman just did so well at making it his own.