I found most of the CPL and IR reasonably straightforward, but I was rubbish at flying a raw-data ILS. Really rubbish, to the point where it became a mindset problem, rather than a lack of flying ability. After a year flying airliners, I'm still rubbish at them, as I proved to myself the other week when I tried one and ended up looking out of the window for inspiration . . .
The good news is that it doesn't matter very much, as 90% of approaches are auto-coupled (the way the company likes it) and on the odd occasion when we do hand fly - usually for practice - it's either fully visual, or an ILS using the flight director. If I'd known that during IR training, I could have saved myself an awful lot of sleepless nights. (And before anyone phones the Daily Mail with a scoop about incompetent airline pilots, I've jumped through quite enough hoops to prove I can safely transport joe public from A to B, thank you very much).
Being an airline pilot is about much, much more than raw flying ability. Being able to function as part of a team, communication, prioritising and managing workload, and not p*ssing off the bloke sat next to you are all at least as important as being able to ace the needles. The vast majority of my colleagues are bloody good at what they do, but that's not because they're brilliant, instinctive stick and rudder pilots. It's because they're professional, conscientious, and put in a lot of effort to stay that way. No-one is perfect, and we all have one or more aspects of our flying that could be improved - that's one of the challenges that keeps the job so fresh. As JB007 pointed out, you'll have good and bad days at the office (and in the sim) throughout your career - it comes with the territory.
Remember that, and you'll appreciate that training difficulties are just part of the learning process. They're not the be-all and and-all that they sometimes appear.