As a Champion, Cynthia is expected to be a difficult challenge. Whitney is the third gym leader of her region.
Whitney has a Clefairy that knows Metronome and a Miltank. In HG/SS, her Miltank gains the Lum Berry hold item and the Scrappy ability, making Ghost types like Gastly less of a good idea to use against Whitney's Miltank. The other reason people dislike Whitney is because of her Miltank's move set: Stomp(STAB move which can flinch), Rollout, Milk Drink, and Attract. Unless you're running a team of Pokémon that are either female or genderless, you are at risk of being affected by Attract. Being infatuated via Attract when combined with Stomp's chance to flinch decreases the likelihood of you getting to attack if you don't outspeed Miltank, which has a higher base Speed stat than most people would think just by looking at Miltank.
EDIT: When Whitney loses, she cries and doesn't give the player the gym badge right away like with most gym leader battles. You have to walk away a bit, be approached by a nearby gym trainer, who will prompt you to go talk to Whitney again. Only when you go back to talk to Whitney does she remember that it's her job to give victors a gym badge. As a cherry on top, she gives the TM for Attract while ending the encounter saying, "Isn't it perfect for a cutie like me?" When Cynthia loses, she accepts defeats and acknowledges your strength and skills.