"He said I may not like the horse when I am done with him."
When the owner is done with him, nothing to do with the trainer or training.
What he/she said was that the OP may not like the horse after having spent all that time and money on the horse. The trainer was simply presenting a good and honest question any owner should consider, about whether or not it would be wise to spend a lot of money on a rescue horse with unknown health, behavior, breeding, and history. Who can say that is not true? Who has not had a horse they were not happy with after all their time and effort? What competitive rider has not sold a horse because the horse just didn't measure up? What serious rider has not worried that their new horse might not fit the bill and be worth all the time, money, and effort? I'd put more trust in a trainer who tried to help me make a wise choice than one who is interested in nothing more than lining their own pockets.
Heather, I wouldn't be too concerned about your trainer. However, if you are going to pay for the training, get a list of a few of his/her former customers and give them a call, or go see them. Find out whether they were happy with the results. Don't forget, there's always that "knowitall" oddball who is never happy with anything. In our area, $4-600/month for basic boarded training is common.
Find out what goes with it and compare. What you normally get is pasture/hay, training/riding a specified number of times per week, and a target goal for what your horse should be able to do reliably at the end of the training. After two months, it will likely be something like walk-trot-canter, some degree of trail desensitization, crossing water (puddles and streams), and trailering. It should be a reliably broke horse who can do simple trail rides safely.
I wholeheartedly agree with those who have said that having the horse trained for you would be the best way to go. But if you decide to do it yourself, you can do it. Even after the horse has been well-trained, if you don't know what you're doing, you'll undo all that good training and it will be wasted money. So, either way, you have some learning to do. You are a trainer every time you ride, whether you want to be or not.
Yep, Waynesboro is about 2 hours, or a little more, from me. A little far to just pop down to help. In another month or so, I could take him and get him started for you, but you'd have to get all the vet checks and spring shots done first and I'd expect you to help out on feed, since I split feed costs with a neighbor. I'd have to keep the horse up here for a month or so. If you're interested, PM me.