Vox considers two options for why Donald Trump is now ahead in the polls:
1) It's just a blip because he's locked up his contest and she's still fighting Bernie.
2) It heralds a "nail-bitingly close" election.
Here's a third possibility you haven't considered: maybe she'll perform exactly the way she's performed against every other opponent, and lose ground in the polls more the longer the contest goes on. Clinton was way ahead of Sanders... but has lost ground steadily against him. She was way ahead of Obama in 2008... but lost ground steadily against him. Now that people are thinking in terms of Trump and Clinton, she's fading against him like she fades against everyone.
He's just now starting to turn his guns on her. By November, this may not be close at all.