How can we use the three sociological paradigms to help solve the problem with the football players disrespecting the flag by kneeling? The three paradigms are structural functionalism, conflict theory, and symbolic interactionism.

One of the powerful aspects of being a sociologist is the ability to analyze various social phenomena from different perspectives. Paradigms provide sociologists with a framework from which to orient themselves philosophically and to analyze society. The three primary paradigms used today include structural functionalism, symbolic interactionism, and conflict theory.
Before we analyze the current event you have mentioned, let's acknowledge something: this event will be viewed vastly differently from these different perspectives. In some of these paradigms, the football players' kneeling will be considered, as you have written, as an act of disrespect toward the flag; however, in other perspectives, the kneeling will be viewed as an empowered act of social change. Please remember to keep an open mind when considering this event from all three perspectives.
Structural functionalism, also known as the functionalist perspective, views all parts of society as interdependent and as providing necessary contribution to the holistic (or "whole") functioning of that society. This perspective is often criticized as being complicit in maintaining the status quo; in other words, it does not motivate members of society to actively change their social environment, even when doing so will directly benefit them. From this perspective, social change is, in fact, undesirable, because it operates on the belief that other parts of society will organically compensate for issues that arise.
In viewing the current event of football players kneeling during the national anthem through the lens of structural functionalism, the answer to this "problem" would be to end acts of social activism during football games. Functionalists would see this act—which began with Colin Kaepernick of the San Francisco 49ers taking a knee during the national anthem to protest police brutality against black Americans—as a futile and undesired action against an issue that should be allowed to be organically solved by society, believing that everything will "work itself out."
The conflict perspective is far more focused on the ever-changing nature of society and the negative conflicts that impact. This perspective advocates for social change (which eventually results in social revolution) in order to prevent the wealthy and powerful from taking advantage of the poor and weak. It acknowledges that the diversity between groups (in terms of gender, socioeconomics, race, politics, etc.) causes these groups to compete against each other to uphold their opposing values. Viewing the kneeling football players from the conflict perspective, we would see their act as a significant act of outcry against inequality—one that is natural given the opposition between the polarized difference between black and white Americans. This perspective would not see this event as particularly surprising or astounding and would allow it to continue, understanding that society is ever-shifting. They would not see it as disrespect for the flag but rather as an organic part of cooperation to impact social change.
The symbolic interactionist paradigm views society with an emphasis on the symbolic, acknowledging that humans attach meanings to symbols and act according to their interpretation of these symbols. This perspective interprets words as requiring intention and interpretation and views dialogue as the interaction of symbols. A symbol within this context can be anything that represents something other than its literal self. From this perspective, the most interesting part of the players kneeling would be how it impacts the symbol of the American flag—a symbol of patriotism, freedom, democracy, and liberty, but also of free speech. Some may argue through this perspective that kneeling during the national anthem is a sign of disrespect to what the flag represents. What's interesting about this interpretation is related to a criticism of this paradigm—that the focus on symbols neglects the influence of institutions and social forces on how an individual may choose to behave. For example, rather than intending to insult the flag and what it represents, perhaps these football players are merely reacting to the institutions around them (say, the militarization of police forces, the Trump administration, etc.) and social forces (the growth of the Black Lives Matter movement).