With a lot of patience. Once the animal tolerates you walking by the cage, changing the water bowl, feeding, and cleaning, you can try and touch it gently or even catch and hold it. If you pay attention to your animal, you will learn when it is comfortable and when not. Start by holding it for a few minutes at a time, a few times a day, and just picking it up, not holding and restraining it. The Hypothalamus is the part of the brain where most of our emotions come from.
All reptiles have one, so they have feelings.
The most basic emotions are fear, aggression, and pleasure. I don't think anyone will argue, that reptiles don't have these feelings and express them. They avoid what they fear, attack what makes them angry, and seek out what is pleasurable. If you create an environment that is comfortable and pleasant, and you do things to your pet that make it feel comfortable and pleased, then the reptile will 'like' you in the sense that good things come from you, and therefore it wants to be with you. Whether reptiles have more complex feelings, like 'liking', is a hard question, and I would give a guarded 'yes' for chelonians, but I don't know about others.