The cartoon obviously portrays this as an example of Islamophobia, but is it, and how can we tell or be sure?
There was a history of Islamophobia in Irving, Texas stemming from February 2015 when right wing Christians and others stirred up fear about Shariah Law Courts being set up. In reality, there was a non-binding, voluntary arbitration service provided by a local mosque and other mosques in the Dallas area. Such arbitration services have been common in Jewish and Christian practice as well, so they are nothing new [1,3]
The mayor, Beth Van Duyne spoke with various conservative pundits, stating that Shariah courts had been set up and touting her support of legislation, “American laws for American courts”, that would prevent Shariah law from being applied in her community. She gave interviews to Dana Loesch and Glenn Beck. She also spoke with Frank Gaffney on the subject, “the founder of the anti-Muslim think tank Center for Security Policy”  [I’m not familiar with this group’s work]. Other articles give more details, including how she benefited from increased fundraising after becoming a national figure because of this issue and how the editorial board of her local paper that had endorsed her called her out on Islamophobia [2, 3, 4].
I think the English teacher who reported the clock as a potential bomb because she was scared was within her rights and duty. I would like to think that she shouldn’t have been scared, but apparently she was so I suppose she had to do something. But, I don’t understand how the situation wasn’t cleared up more quickly without involving the police or at least without resorting to handcuffs, detention at a juvenile facility, and fingerprinting. To be clear, the police said they quickly knew it wasn’t a bomb and they were instead investigating whether or not Ahmed intended to scare people with a fake bomb, which is illegal.
The Irving police chief, Larry Boyd, gave an interview on CNN and said that the police weren’t initially aware that Ahmed had told multiple people about his clock project that day and that his engineering or robotics teacher had seen it and understood what it was. Once they had these facts, they were able to determine that there was no bomb hoax and that Ahmed did not do anything to make people afraid .
I’m not sure why they didn’t have these facts right away from the principal’s and other school staff’s inquiries. Quoting Police Chief Boyd:
“There were factors and details to this that for whatever reason weren’t shared with the officers who were there initially. So as we pursued this investigation further — as you know we didn’t file any charges on him — we dropped those charges because we were able to find out those facts that you’re [the CNN host] referring to. Yeah, he did talk to people earlier and presented it as you described [as a clock, an engineering project]. Those were the kinds of things that allowed us to settle the matter” .
Another interesting take on this comes from  which asserts that public schools all over the country are becoming too strict and paranoid, with zero tolerance laws that unfairly mete out severe punishment to both white and minority kids. It also makes the case that liberals tend to jump to explanations for severe punishment based on race or Islamophobia when the larger problem of zero tolerance and safety paranoia is to blame.
That author writes
I accept that it’s perfectly plausible—if not yet definitively proven—racism played a role in the specific case of Ahmed Muhamed [sic]. And it’s certainly true that poor and minority youths are at greater risk of mistreatment. Studies show schools discipline black and Latino kids more harshly and more frequently than white kids who commit the same offenses. [My note: also see references 7,8]
But it would be a grave mistake to zero-in on racism as the main problem here, because ridiculous over-enforcement of school disciplinary policies is only partly a race issue. No child is safe from having his or her rights’ trampled by assertive cops at school as long as paranoia about school safety and petty rules outlawing perfectly safe, normal teen behavior remain in place. Cops arrest kids for bringing harmless toys that vaguely resemble weapons to school. Schools suspend kids for talking, writing, or merely just thinking about said weapons while on school premises, or near school premises, or even just near the bus stop on their own front lawns.” 
So basically this article is saying that Islamophobia or race could be a contributing factor, and I think it was. I think it’s a distraction to argue whether this incident was purely about Islamophobia, but I just can’t fathom the thought that Islamophobia or fear of another culture, religion, or skin color played absolutely no part somewhere in the whole chain of events.
Fortunately, Ahmed has been receiving a lot of support from notable people including the President, and has even gotten some sweet swag for his troubles.
Finally, I want to end on a quick note about Islamphobia and racism. People argue over these terms as applied to cases like this, noting Islam is a religion, not a race, so Islamophobia is different from racism. I think they’re related because some roots of Islamophobia stem from the fact that many Muslims are from the Middle East and are not white. Fear is often based on differences between people and unconscious or conscious labeling of people as “the Other”. People are “Others” because of differences in culture, race, appearance, religion, and other factors.