Thaddeus's answer is, by far, the most important one here.
Two more things that I wanted to point out, though:
The Flash's powers are almost universally deliberate actions. Unlike Superman, who is bulletproof even when he's having a quiet dinner as Clark Kent, the Flash has to BECOME intangible, or CHOOSE to travel through time, etc. It's something he has to realize is necessary, and then he has to actually activate the power. His reflexes and accelerated healing are (almost) always "on," but everything else is an action he must begin, not a standing truth about him at all times. That means that a potential exists for them to be nullified or prevented.
Because of this, as Thaddeus so eloquently said, many of Flash's foes focus on confusion, misdirection, ambush, unpredictability, or other factors that limit the Flash's ability to USE his powers. Batman's enemies often seem to think that they can actually beat him outright, but the Rogues (at least the non-speedsters) almost never try to beat the Flash through superior speed or force. Instead, they try to keep him off-balance enough that he can't make full use of his abilities.
Because of this, the hope springs eternal in the mind of every one of the Rogues: "if I can just ___________, he'll be helpless!"
And secondly, many of Flash's powers are often shown to be difficult, exhausting, or dangerous to use. He can travel in time, sure, as long as he doesn't mind risking an unexpected change that could ruin the whole universe (like in Flashpoint/Flashpoint Paradox). Becoming intangible is often shown to require a moment of preparation and a "deep breath" before he starts, as though maintaining that vibration isn't as easy as, say, Martian Manhunter's effortless intangibility. (Some Flashes don't even have the ability to vibrate into intangibility, it's so difficult.) His predictive abilities are nice, but in many versions they require him to recognize that something needs to be predicted: they often aren't like Peter Parker's spider-sense, which goes off even if he thinks nothing is wrong. And oftentimes, the upper-limit of his abilities can damage even him: on numerous occasions the Flash has moved so fast he's almost merged with the Speed Force and died, or aged himself to the brink of death, etc.
Therefore, while the Flash is an incredibly potent superhero, the Rogues have learned to take advantage of his weaknesses and the Flash himself has to be careful not to over-do it with his own powers.