Why doesn't the Mosasaurus attack the audience since we know it can reach them?

I do not believe we can definitively answer this question. It refers to an extinct animal used in a movie for a specific plot reason: to resolve the conflict at the climax of the movie. We do not know how Mosasaurus would react in either of its feeding scenarios presented in the movie.

However, we can apply logic and see where it takes us.

The amphitheater scene

During this scene, the announcer specifically mentions the dinosaur is shy and may not be hungry. Most predators across the entire animal kingdom are more aggressive when hungry. While it may not be exactly safe to approach a satiated predator such as a wild lion, it is certainly more dangerous to approach one that is very hungry.

If the animal handlers at Jurassic World keep the Mosasaurus well-fed, it should keep it relatively more docile.

Also keep in mind that this is a purely aquatic predator that lives entirely in water: going after "land meat" is possible, but unlikely. While it is relatively easy for e.g. bears to pick fish from a stream, it would be more difficult for e.g. a shark to come on shore and eat a human.

Finally, there is a size consideration. Mosasaurus could flop into the stands, but those seats are set back a bit from the water, and humans are much smaller than it. Why go after tiny prey that is difficult to reach when larger prey is practically hand-fed on a regular basis?

The boardwalk scene

At the end of the movie, Indominus and T-Rex are fighting and eventually they back Indominus up against the fence by the water.

Three factors are different here compared to earlier in the movie:

1. Mosasaurus is likely to be hungrier. The panic in the park meant it may not have eaten in hours. A carnivore that size must each a substantial amount of meat just to have enough energy to live. It is likely to be on the more aggressive end of its behavior scale.

2. The prey is closer. Remember, they are at the boardwalk now, and Indominus is up against the fence. Earlier, the humans were sitting further away from the fence. This means that the prey will be easier to see: an object sticking up from the boardwalk is easier to see from underwater than prey further away, blending into the shape of the amphitheater.

3. The prey is larger. One human might be a tiny snack, but Indominus is a full meal. If Mosasaurus is hungry (see point 1), this would clinch the deal. This also makes the prey easier to see: for a large animal such as Mosasaurus, the Indominus is easier to see from underwater than humans are. This would be similar to how a dog is easier for a human to see than a hundred ants.

Conclusion

Based on common-sense and logic, it is reasonable to assume that Mosasaurus would largely ignore the human audience while attacking Indominus.

A mostly satiated Mosasaurus would ignore tiny prey set back from the water, while attacking the large prey standing on the edge of the water when hungry.

It was hungry, with a large, loud, distract, and injured prey within reach.

1. It has gone at least half a day without being fed.

2. The Indominus Rex is louder by multiple orders of magnitude than the crowd, a single point of sound, and likely in the right hearing range of the Mosasaurus.

3. The Indominus is distracted. Ambush predators take their prey's attention in mind when deciding when and how to attack. A wary animal is harder to attack then one with its defences down. Indominus was not paying attention to the water, giving the Mosasaurus opportunity to attack.

4. Indominus is Injured and bleeding. The scent of blood would tempt the Mosasaurus greatly.

5. Most Importantly, it wouldn't attack the crowd, when it has a free meal dangling right above it. It goes for the easy kill.

Keep in mind that all dinosaurs at Jurassic Park/World have been genetically engineered for fun and profit. They don't look like they used to, and were changed to fit public (mis)conceptions about how they are supposed to look and act. The Mosasaurus in Jurassic World is freaking huge compared to a natural one. The largest real one has a mouth a bit longer than a human, roughly 10 feet long, while the movie one is as long as a Great White Shark, typically 20 feet long. And it may have habits that are not common for a real one. Scientific belief is that it ate other marine dinosaurs, not ambush land ones. See https://en.wikipedia.org/wiki/Mosasaurus

According to me, there is another possibility here. We can see the electrical fences in the first shot. But there was no electricity when Mosasaurus drags Indominous Rex. Probably, that made easier for Mosasaurus to attack Indominous instead of humans.

According to the comment by @snowman, we can only presume the behavior of Mosasaurus based on other animals. Other animals are afraid of electrical fences (as shown in Jurassic Park and Jurassic World). Based on that assumption, we can conclude that Mosasaurus could not have attacked while there are electrical fences.